PDB_ID PUBMED_CID STRUCTURE TITLE DEPOSITION DATE RELEASE DATE AUTHORS CITATION TITLE JOURNAL YEAR VOLUME FIRST PAGE LAST PAGE 3V6A 22334682 Helical repeat structure of apoptosis inhibitor 5 reveals protein-protein interaction modules 2011-12-19 2012-02-22 Han, B.G.,Kim, K.H.,Lee, S.J.,Jeong, K.C.,Cho, J.W.,Noh, K.H.,Kim, T.W.,Kim, S.J.,Yoon, H.J.,Suh, S.W.,Lee, S.H.,Lee, B.I. Helical repeat structure of apoptosis inhibitor 5 reveals protein-protein interaction modules. J.Biol.Chem. 2012 287 10727 10737 3U3T 22525750 The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6) 2011-10-06 2012-05-02 Ru, H.,Zhao, L.X.,Ding, W.,Jiao, L.Y.,Shaw, N.,Liang, W.,Zhang, L.G.,Hung, L.W.,Matsugaki, N.,Wakatsuki, S.,Liu, Z.J. S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS Acta Crystallogr.,Sect.D 2012 68 521 530 3U3V 22525750 The S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6) 2011-10-06 2012-05-02 Ru, H.,Zhao, L.X.,Ding, W.,Jiao, L.Y.,Shaw, N.,Liang, W.,Zhang, L.G.,Hung, L.W.,Matsugaki, N.,Wakatsuki, S.,Liu, Z.J. S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS Acta Crystallogr.,Sect.D 2012 68 521 530 3VSL 22846910 Crystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant Staphylococcus aureus in the cefotaxime bound form. 2012-04-25 2012-10-31 Yoshida, H.,Kawai, F.,Obayashi, E.,Akashi, S.,Roper, D.I.,Tame, J.R.,Park, S.Y. Crystal Structures of Penicillin-Binding Protein 3 (PBP3) from Methicillin-Resistant Staphylococcus aureus in the Apo and Cefotaxime-Bound Forms. J.Mol.Biol. 2012 423 351 364 3VTT 23239402 High Resolution crystal structure of Dengue 3 Envelope protein domain III (ED3) 2012-06-07 2012-12-26 Elahi, M.,Islam, M.M.,Noguchi, K.,Yohda, M.,Kuroda, Y. High resolution crystal structure of dengue-3 envelope protein domain III suggests possible molecular mechanisms for serospecific antibody recognition Proteins 2013 81 1090 1095 3VR6 23334411 Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1] 2012-04-03 2013-01-16 Arai, S.,Saijo, S.,Suzuki, K.,Mizutani, K.,Kakinuma, Y.,Ishizuka-Katsura, Y.,Ohsawa, N.,Terada, T.,Shirouzu, M.,Yokoyama, S.,Iwata, S.,Yamato, I.,Murata, T. Rotation mechanism of Enterococcus hirae V(1)-ATPase based on asymmetric crystal structures Nature 2013 493 703 707 3VUY 23032187 Crystal structure of A20 ZF7 in complex with linear tetraubiquitin 2012-07-09 2013-02-13 Tokunaga, F.,Nishimasu, H.,Ishitani, R.,Goto, E.,Noguchi, T.,Mio, K.,Kamei, K.,Ma, A.,Iwai, K.,Nureki, O. Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-kappaB regulation Embo J. 2012 31 3856 3870 4GSU 23519417 Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains 2012-08-28 2013-02-27 Kim, H.S.,Kim, J.,Im, H.N.,Yoon, J.Y.,An, D.R.,Yoon, H.J.,Kim, J.Y.,Min, H.K.,Kim, S.-J.,Lee, J.Y.,Han, B.W.,Suh, S.W. Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains Acta Crystallogr.,Sect.D 2013 69 420 431 3VQG Crystal Structure Analysis of the PDZ Domain Derived from the Tight Junction Regulating Protein 2012-03-23 2013-03-27 Akiyoshi, Y.,Nakakura, Y.,Hamada, D.,Goda, N.,Tenno, T.,Narita, H.,Nakagawa, A.,Furuse, M.,Suzuki, M.,Hiroaki, H. Structural basis for down regulation of tight junction by PDZ-domain containing E3-Ubiquitin ligase To be Published 0 0 0 0 4HAB 23498919 Crystal structure of Plk1 Polo-box domain in complex with PL-49 2012-09-26 2013-04-03 Murugan, R.N.,Park, J.E.,Lim, D.,Ahn, M.,Cheong, C.,Kwon, T.,Nam, K.Y.,Choi, S.H.,Kim, B.Y.,Yoon, D.Y.,Yaffe, M.B.,Yu, D.Y.,Lee, K.S.,Bang, J.K. Development of cyclic peptomer inhibitors targeting the polo-box domain of polo-like kinase 1. Bioorg.Med.Chem. 2013 21 2623 2634 4HY2 23498919 Crystal structure of Plk1 Polo-box domain in complex with PL-42 2012-11-12 2013-04-03 Murugan, R.N.,Park, J.E.,Lim, D.,Ahn, M.,Cheong, C.,Kwon, T.,Nam, K.Y.,Choi, S.H.,Kim, B.Y.,Yoon, D.Y.,Yaffe, M.B.,Yu, D.Y.,Lee, K.S.,Bang, J.K. Development of cyclic peptomer inhibitors targeting the polo-box domain of polo-like kinase 1. Bioorg.Med.Chem. 2013 21 2623 2634 4IGA 23237794 The crystal structure of an activated Thermotoga maritima CheY with N-terminal region of FliM 2012-12-17 2013-04-24 Ahn, D.R.,Song, H.,Kim, J.,Lee, S.,Park, S.Y. The crystal structure of an activated Thermotoga maritima CheY with N-terminal region of FliM. Int.J.Biol.Macromol. 2013 54 76 83 3VS7 23596204 Crystal structure of HCK complexed with a pyrazolo-pyrimidine inhibitor 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine 2012-04-21 2013-05-01 Saito, Y.,Yuki, H.,Kuratani, M.,Hashizume, Y.,Takagi, S.,Honma, T.,Tanaka, A.,Shirouzu, M.,Mikuni, J.,Handa, N.,Ogahara, I.,Sone, A.,Najima, Y.,Tomabechi, Y.,Wakiyama, M.,Uchida, N.,Tomizawa-Murasawa, M.,Kaneko, A.,Tanaka, S.,Suzuki, N.,Kajita, H.,Aoki, Y.,Ohara, O.,Shultz, L.D.,Fukami, T.,Goto, T.,Taniguchi, S.,Yokoyama, S.,Ishikawa, F. A Pyrrolo-Pyrimidine Derivative Targets Human Primary AML Stem Cells in Vivo Sci Transl Med 2013 5 0 0 4EXT Structure of polymerase-interacting domain of human Rev1 in complex with translesional synthesis polymerase zeta 2012-05-01 2013-05-08 Liu, D.N.,Ryu, K.S.,Ko, J.S.,Choi, B.S. Insights into the scaffold mechanism of human Rev1 in translesional synthesis revealed by structural studies on its polymerase-interacting domain To be Published 0 0 0 0 4FYC 23633582 Structural and functional characterizations of a thioredoxin-fold protein from Helicobacter pylori 2012-07-04 2013-05-08 Yoon, J.Y.,Kim, J.,An, D.R.,Lee, S.J.,Kim, H.S.,Im, H.N.,Yoon, H.J.,Kim, J.Y.,Kim, S.J.,Han, B.W.,Suh, S.W. Structural and functional characterization of HP0377, a thioredoxin-fold protein from Helicobacter pylori Acta Crystallogr.,Sect.D 2013 69 735 746 3W6D 23658014 Crystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E141Q) in complex with tetrasaccharide 2013-02-14 2013-05-15 Arimori, T.,Kawamoto, N.,Shinya, S.,Okazaki, N.,Nakazawa, M.,Miyatake, K.,Fukamizo, T.,Ueda, M.,Tamada, T. Crystal Structures of the Catalytic Domain of a Novel Glycohydrolase Family 23 Chitinase from Ralstonia sp. A-471 Reveals a Unique Arrangement of the Catalytic Residues for Inverting Chitin Hydrolysis J.Biol.Chem. 2013 288 18696 18706 4HYQ 23416196 Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297 2012-11-14 2013-05-29 Murayama, K.,Kano, K.,Matsumoto, Y.,Sugimori, D. Crystal structure of phospholipase A1 from Streptomyces albidoflavus NA297 J.Struct.Biol. 2013 182 192 196 4G4W Crystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii 2012-07-16 2013-07-24 Lee, W.C.,Park, J.S.,Song, J.H.,Kim, S.I.,Lee, J.C.,Cheong, J.,Kim, H.Y. Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA to be published 0 0 0 0 3VWD Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 in complex with acetoacetyl-CoA (P21212 form) 2012-08-22 2013-08-28 Yuzawa, S.,Sumimoto, H. Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 To be Published 0 0 0 0 3VWE Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 in complex with CoA (P21 form) 2012-08-22 2013-08-28 Yuzawa, S.,Sumimoto, H. Crystal structure of alpha-tubulin acetyltransferase domain of human Mec-17 To be Published 0 0 0 0 3VZP 23913421 Crystal structure of PhaB from Ralstonia eutropha 2012-10-15 2013-08-28 Matsumoto, K.,Tanaka, Y.,Watanabe, T.,Motohashi, R.,Ikeda, K.,Tobitani, K.,Yao, M.,Tanaka, I.,Taguchi, S. Directed evolution and structural analysis of NADPH-dependent Acetoacetyl Coenzyme A (Acetoacetyl-CoA) reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics Appl.Environ.Microbiol. 2013 79 6134 6139 3WEU 23908359 Crystal structure of the L-Lys epsilon-oxidase from Marinomonas mediterranea 2013-07-12 2013-09-04 Okazaki, S.,Nakano, S.,Matsui, D.,Akaji, S.,Inagaki, K.,Asano, Y. X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea J.Biochem. 2013 154 233 236 4KL0 24007778 Crystal structure of the effector protein XOO4466 2013-05-07 2013-10-09 Yu, S.,Hwang, I.,Rhee, S. 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J.Am.Chem.Soc. 2013 135 15526 15535 4L4Z 24047255 Crystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different analogs reveal distinct mechanisms for ligand recognition 2013-06-10 2013-11-06 Ha, J.H.,Eo, Y.,Grishaev, A.,Guo, M.,Smith, J.A.,Sintim, H.O.,Kim, E.H.,Cheong, H.K.,Bentley, W.E.,Ryu, K.S. Crystal Structures of the LsrR Proteins Complexed with Phospho-AI-2 and Two Signal-Interrupting Analogues Reveal Distinct Mechanisms for Ligand Recognition. J.Am.Chem.Soc. 2013 135 15526 15535 4L50 24047255 Crystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different analogs reveal distinct mechanisms for ligand recognition 2013-06-10 2013-11-06 Ha, J.H.,Eo, Y.,Grishaev, A.,Guo, M.,Smith, J.A.,Sintim, H.O.,Kim, E.H.,Cheong, H.K.,Bentley, W.E.,Ryu, K.S. Crystal Structures of the LsrR Proteins Complexed with Phospho-AI-2 and Two Signal-Interrupting Analogues Reveal Distinct Mechanisms for Ligand Recognition. J.Am.Chem.Soc. 2013 135 15526 15535 4L5J 24047255 Crystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different analogs reveal distinct mechanisms for ligand recognition 2013-06-11 2013-11-06 Ha, J.H.,Eo, Y.,Grishaev, A.,Guo, M.,Smith, J.A.,Sintim, H.O.,Kim, E.H.,Cheong, H.K.,Bentley, W.E.,Ryu, K.S. Crystal Structures of the LsrR Proteins Complexed with Phospho-AI-2 and Two Signal-Interrupting Analogues Reveal Distinct Mechanisms for Ligand Recognition. J.Am.Chem.Soc. 2013 135 15526 15535 3WJJ 23744091 Crystal structure of IIb selective Fc variant, Fc(P238D), in complex with FcgRIIb 2013-10-10 2013-11-13 Mimoto, F.,Katada, H.,Kadono, S.,Igawa, T.,Kuramochi, T.,Muraoka, M.,Wada, Y.,Haraya, K.,Miyazaki, T.,Hattori, K. Engineered antibody Fc variant with selectively enhanced Fc gamma RIIb binding over both Fc gamma RIIaR131 and Fc gamma RIIaH131. Protein Eng.Des.Sel. 2013 26 589 598 3WKQ Copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with formate 2013-10-29 2013-12-11 Fukuda, Y.,Inoue, T. Copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with formate to be published 0 0 0 0 4LKM 24223211 Crystal structure of Plk1 Polo-box domain in complex with PL-74 2013-07-08 2013-12-11 Murugan, R.N.,Ahn, M.,Lee, W.C.,Kim, H.Y.,Song, J.H.,Cheong, C.,Hwang, E.,Seo, J.H.,Shin, S.Y.,Choi, S.H.,Park, J.E.,Bang, J.K. Exploring the binding nature of pyrrolidine pocket-dependent interactions in the polo-box domain of polo-like kinase 1 Plos One 2013 8 0 0 3WC2 24324136 Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG) 2013-05-24 2013-12-18 Nakamura, A.,Nemoto, T.,Heinemann, I.U.,Yamashita, K.,Sonoda, T.,Komoda, K.,Tanaka, I.,Soll, D.,Yao, M. 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Nature 2017 551 521 524 5XZQ 29155493 Hydroxynitrile lyase from Passiflora edulis (PeHNL) 2017-07-13 2017-11-22 Motojima, F.,Nuylert, A.,Asano, Y. The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis FEBS J. 2018 285 313 324 5XZT 29155493 C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) 2017-07-13 2017-11-22 Motojima, F.,Nuylert, A.,Asano, Y. The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis FEBS J. 2018 285 313 324 5Y02 29155493 C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile 2017-07-14 2017-11-22 Motojima, F.,Nuylert, A.,Asano, Y. 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Nat Commun 2021 12 6294 6294 7D6Q 33972673 Crystal structure of the Stx2a 2020-10-01 2021-04-14 Watanabe-Takahashi, M.,Tamada, M.,Senda, M.,Hibino, M.,Shimizu, E.,Okuta, A.,Miyazawa, A.,Senda, T.,Nishikawa, K. Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin. Commun Biol 2021 4 538 538 7C5V 34006275 Crystal structure of the iota-carbonic anhydrase from cyanobacterium complexed with bicarbonate 2020-05-20 2021-04-28 Hirakawa, Y.,Senda, M.,Fukuda, K.,Yu, H.Y.,Ishida, M.,Taira, M.,Kinbara, K.,Senda, T. Characterization of a novel type of carbonic anhydrase that acts without metal cofactors. Bmc Biol. 2021 19 105 105 7C5X 34006275 Crystal structure of the iota-carbonic anhydrase from eukaryotic microalga complexed with bicarbonate 2020-05-20 2021-04-28 Hirakawa, Y.,Senda, M.,Fukuda, K.,Yu, H.Y.,Ishida, M.,Taira, M.,Kinbara, K.,Senda, T. Characterization of a novel type of carbonic anhydrase that acts without metal cofactors. 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Design of complicated all-alpha protein structures Nat.Struct.Mol.Biol. 2024 0 0 0 7COK 34309403 Crystal structure of ligand-free form of 5-ketofructose reductase of Gluconobacter sp. strain CHM43 2020-08-04 2021-08-04 Nguyen, T.M.,Goto, M.,Noda, S.,Matsutani, M.,Hodoya, Y.,Kataoka, N.,Adachi, O.,Matsushita, K.,Yakushi, T. The 5-Ketofructose Reductase of Gluconobacter sp. Strain CHM43 Is a Novel Class in the Shikimate Dehydrogenase Family. J.Bacteriol. 2021 203 0 0 7DBM 34076480 HIV-1 reverse transcriptase mutant Q151M/Y115F/F116Y/M184V:DNA:dGTP ternary complex 2020-10-21 2021-08-04 Nakajima, S.,Watashi, K.,Kato, T.,Muramatsu, M.,Wakita, T.,Tamura, N.,Hattori, S.I.,Maeda, K.,Mitsuya, H.,Yasutake, Y.,Toyoda, T. Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations. 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The ligand-free structure of human PPARgamma LBD To Be Published 0 0 0 0 7FG6 34461441 Crystal structure of the Tyrosyl-tRNA synthetase (TyrRS) in Nanoarchaeum equitans 2021-07-26 2021-09-08 Horikoshi, T.,Noguchi, H.,Umehara, T.,Mutsuro-Aoki, H.,Kurihara, R.,Noguchi, R.,Hashimoto, T.,Watanabe, Y.,Ando, T.,Kamata, K.,Park, S.Y.,Tamura, K. Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA Tyr with an extra guanosine residue at the 5'-terminus. Biochem.Biophys.Res.Commun. 2021 575 90 95 7E98 34804547 Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen saturation 2021-03-03 2021-10-06 Numoto, N.,Kawano, Y.,Okumura, H.,Baba, S.,Fukumori, Y.,Miki, K.,Ito, N. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. 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J.Exp.Med. 2021 218 0 0 7DC5 33727595 Crystal structure of fungal antifreeze protein with intermediate activity 2020-10-23 2021-10-27 Khan, N.M.U.,Arai, T.,Tsuda, S.,Kondo, H. Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. Sci Rep 2021 11 5971 5971 7DDB 33727595 Crystal structure of fungal antifreeze protein with intermediate activity 2020-10-28 2021-11-03 Khan, N.M.U.,Arai, T.,Tsuda, S.,Kondo, H. Characterization of microbial antifreeze protein with intermediate activity suggests that a bound-water network is essential for hyperactivity. Sci Rep 2021 11 5971 5971 7EXZ 34728636 DgpB-DgpC complex apo 2.5 angstrom 2021-05-29 2021-11-03 Mori, T.,Kumano, T.,He, H.,Watanabe, S.,Senda, M.,Moriya, T.,Adachi, N.,Hori, S.,Terashita, Y.,Kawasaki, M.,Hashimoto, Y.,Awakawa, T.,Senda, T.,Abe, I.,Kobayashi, M. 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Angew.Chem.Int.Ed.Engl. 2022 61 0 0 7DQR Crystal structure of Sulfurisphaera tokodaii methylated O6-methylguanine methyltransferase 2020-12-24 2021-12-15 Kikuchi, M.,Yamauchi, T.,Iizuka, Y.,Tsonoda, M. Roles of the hydroxy group of tyrosine in crystal structures of Sulfurisphaera tokodaii O6-methylguanine-DNA methyltransferase. Acta Crystallogr.,Sect.F 2021 77 444 451 7F36 TacT complexed with acetyl-glycyl-tRNAGly 2021-06-15 2021-12-22 Yashiro, Y.,Zhang, C.,Sakaguchi, Y.,Suzuki, T.,Tomita, K. Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium Cell Rep 2021 37 110130 0 7DQD Crystal structure of the AMP-PNP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase 2020-12-23 2021-12-29 Imamura, M.,Maruyama, S.,Nakamoto, K.,Kawai, F.,Akiyama, T.,Mizutani, K.,Suzuki, K.,Shirouzu, M.,Iino, R.,Uchihashi, T.,Ando, T.,Murata, T. The combination of high-speed AFM and X-ray crystallography reveals rotary catalysis To Be Published 0 0 0 0 7DQE Crystal structure of the ADP-bound mutant A(S23C)3B(N64C)3 complex from enterococcus hirae V-ATPase 2020-12-23 2021-12-29 Imamura, M.,Maruyama, S.,Nakamoto, K.,Kawai, F.,Akiyama, T.,Mizutani, K.,Suzuki, K.,Shirouzu, M.,Iino, R.,Uchihashi, T.,Ando, T.,Murata, T. The Combination of High-Speed AFM and X-ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-ATPase To Be Published 0 0 0 0 7E6P 34464082 Fab-amyloid beta fragment complex 2021-02-23 2022-01-05 Kageyama, Y.,Irie, Y.,Matsushima, Y.,Segawa, T.,Bellier, J.P.,Hidaka, K.,Sugiyama, H.,Kaneda, D.,Hashizume, Y.,Akatsu, H.,Miki, K.,Kita, A.,Walker, D.G.,Irie, K.,Tooyama, I. Characterization of a Conformation-Restricted Amyloid beta Peptide and Immunoreactivity of Its Antibody in Human AD brain. Acs Chem Neurosci 2021 12 3418 3432 7WAB 34999257 Crystal structure of the prolyl endoprotease, PEP, from Aspergillus niger 2021-12-14 2022-01-12 Miyazono, K.I.,Kubota, K.,Takahashi, K.,Tanokura, M. Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger. Biochem.Biophys.Res.Commun. 2022 591 76 81 7FFA 35039506 Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis 2021-07-23 2022-01-19 Wang, X.H.,Gao, B.W.,Nakashima, Y.,Mori, T.,Zhang, Z.X.,Kodama, T.,Lee, Y.E.,Zhang, Z.K.,Wong, C.P.,Liu, Q.Q.,Qi, B.W.,Wang, J.,Li, J.,Liu, X.,Abe, I.,Morita, H.,Tu, P.F.,Shi, S.P. Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Nat Commun 2022 13 348 348 7FFC 35039506 Diarylpentanoid-producing polyketide synthase (A210E mutant) 2021-07-23 2022-01-19 Wang, X.H.,Gao, B.W.,Nakashima, Y.,Mori, T.,Zhang, Z.X.,Kodama, T.,Lee, Y.E.,Zhang, Z.K.,Wong, C.P.,Liu, Q.Q.,Qi, B.W.,Wang, J.,Li, J.,Liu, X.,Abe, I.,Morita, H.,Tu, P.F.,Shi, S.P. Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Nat Commun 2022 13 348 348 7FFG 35039506 Diarylpentanoid-producing polyketide synthase (N199F mutant) 2021-07-23 2022-01-19 Wang, X.H.,Gao, B.W.,Nakashima, Y.,Mori, T.,Zhang, Z.X.,Kodama, T.,Lee, Y.E.,Zhang, Z.K.,Wong, C.P.,Liu, Q.Q.,Qi, B.W.,Wang, J.,Li, J.,Liu, X.,Abe, I.,Morita, H.,Tu, P.F.,Shi, S.P. Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Nat Commun 2022 13 348 348 7FFI 35039506 Diarylpentanoid-producing polyketide synthase (F340W mutant) 2021-07-23 2022-01-19 Wang, X.H.,Gao, B.W.,Nakashima, Y.,Mori, T.,Zhang, Z.X.,Kodama, T.,Lee, Y.E.,Zhang, Z.K.,Wong, C.P.,Liu, Q.Q.,Qi, B.W.,Wang, J.,Li, J.,Liu, X.,Abe, I.,Morita, H.,Tu, P.F.,Shi, S.P. Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood. Nat Commun 2022 13 348 348 7W6E 34939812 Polyketide cyclase OAC-F24I mutant from Cannabis sativa in complex with 6-heptylresorcylic acid 2021-12-01 2022-02-02 Lee, Y.E.,Nakashima, Y.,Kodama, T.,Chen, X.,Morita, H. Dual Engineering of Olivetolic Acid Cyclase and Tetraketide Synthase to Generate Longer Alkyl-Chain Olivetolic Acid Analogs. 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Structural insights into recognition of SL4, the UUCG stem-loop, of human U1 snRNA by the ubiquitin-like domain, including the C-terminal tail in the SF3A1 subunit of U2 snRNP. J.Biochem. 2023 174 203 216 8IE5 37171222 Crystal structure of DAPK1 in complex with oxyresveratrol 2023-02-15 2023-05-24 Yokoyama, T.,Kusaka, K. Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1. Febs J. 2023 290 4465 4479 8IE6 37171222 Crystal structure of DAPK1 in complex with pinostilbene 2023-02-15 2023-05-24 Yokoyama, T.,Kusaka, K. Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1. Febs J. 2023 290 4465 4479 8IE7 37171222 Crystal structure of DAPK1 in complex with pterostilbene 2023-02-15 2023-05-24 Yokoyama, T.,Kusaka, K. Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1. 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Nat Commun 2023 14 4752 4752 8GQB 37550286 Crystal structure of lasso peptide epimerase MslH D11A mutant 2022-08-29 2023-06-21 Nakashima, Y.,Kawakami, A.,Ogasawara, Y.,Maeki, M.,Tokeshi, M.,Dairi, T.,Morita, H. Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism. Nat Commun 2023 14 4752 4752 8ITG 37550286 Crystal structure of lasso peptide epimerase MslH in complexed with precursor peptide variant MslAW21G 2023-03-22 2023-06-21 Nakashima, Y.,Kawakami, A.,Ogasawara, Y.,Maeki, M.,Tokeshi, M.,Dairi, T.,Morita, H. Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism. Nat Commun 2023 14 4752 4752 8ITH 37550286 Crystal structure of lasso peptide epimerase MslH H295N 2023-03-22 2023-06-21 Nakashima, Y.,Kawakami, A.,Ogasawara, Y.,Maeki, M.,Tokeshi, M.,Dairi, T.,Morita, H. Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism. Nat Commun 2023 14 4752 4752 8GUZ 37339067 Crystal structure of anti-FIXa IgG fab with FAST-Ig mutations 2022-09-14 2023-06-28 Koga, H.,Yamano, T.,Betancur, J.,Nagatomo, S.,Ikeda, Y.,Yamaguchi, K.,Nabuchi, Y.,Sato, K.,Teranishi-Ikawa, Y.,Sato, M.,Hirayama, H.,Hayasaka, A.,Torizawa, T.,Haraya, K.,Sampei, Z.,Shiraiwa, H.,Kitazawa, T.,Igawa, T.,Kuramochi, T. Efficient production of bispecific antibody by FAST-Ig TM and its application to NXT007 for the treatment of hemophilia A. Mabs 2023 15 2222441 2222441 8GV0 37339067 Crystal structure of anti-FIXa IgG fab without FAST-Ig mutations 2022-09-14 2023-06-28 Koga, H.,Yamano, T.,Betancur, J.,Nagatomo, S.,Ikeda, Y.,Yamaguchi, K.,Nabuchi, Y.,Sato, K.,Teranishi-Ikawa, Y.,Sato, M.,Hirayama, H.,Hayasaka, A.,Torizawa, T.,Haraya, K.,Sampei, Z.,Shiraiwa, H.,Kitazawa, T.,Igawa, T.,Kuramochi, T. Efficient production of bispecific antibody by FAST-Ig TM and its application to NXT007 for the treatment of hemophilia A. Mabs 2023 15 2222441 2222441 8H1L 37314406 Crystal structure of glucose-2-epimerase in complex with D-Glucitol from Runella slithyformis Runsl_4512 2022-10-03 2023-07-12 Wang, H.,Sun, X.,Saburi, W.,Hashiguchi, S.,Yu, J.,Ose, T.,Mori, H.,Yao, M. Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis. Acta Crystallogr D Struct Biol 2023 79 585 595 8IGU 37414880 Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty 2023-02-21 2023-07-12 Kosugi, T.,Iida, T.,Tanabe, M.,Iino, R.,Koga, N. Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Nat.Chem. 2023 15 1591 1598 8IGV 37414880 Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP-Pi)1cat(ADP)2cat,2non-cat 2023-02-21 2023-07-12 Kosugi, T.,Iida, T.,Tanabe, M.,Iino, R.,Koga, N. Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Nat.Chem. 2023 15 1591 1598 8IGW 37414880 Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat 2023-02-21 2023-07-12 Kosugi, T.,Iida, T.,Tanabe, M.,Iino, R.,Koga, N. Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Nat.Chem. 2023 15 1591 1598 8JJS 37463267 Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP10343 2023-05-31 2023-07-26 Tanada, M.,Tamiya, M.,Matsuo, A.,Chiyoda, A.,Takano, K.,Ito, T.,Irie, M.,Kotake, T.,Takeyama, R.,Kawada, H.,Hayashi, R.,Ishikawa, S.,Nomura, K.,Furuichi, N.,Morita, Y.,Kage, M.,Hashimoto, S.,Nii, K.,Sase, H.,Ohara, K.,Ohta, A.,Kuramoto, S.,Nishimura, Y.,Iikura, H.,Shiraishi, T. Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor. J.Am.Chem.Soc. 2023 145 16610 16620 7YM5 Crystal structure of the Salmonella effector SseK1 2022-07-27 2023-08-02 Kim, U.J.,Park, J.B.,Yoo, Y.,Cho, H.S. Crystal structure of the Salmonella effector SseK1 To Be Published 0 0 0 0 7YM7 Crystal structure of the Salmonella effector SseK1 F187A mutant 2022-07-27 2023-08-02 Kim, U.J.,Park, J.B.,Yoo, Y.,Cho, H.S. Crystal structure of the Salmonella effector SseK1 To Be Published 0 0 0 0 7YN1 Crystal structure of selenomethionine labeled CcbD 2022-07-29 2023-08-02 Mori, T.,Kadlcik, S.,Abe, I. Crystal structure of selenomethionine labeled CcbD To Be Published 0 0 0 0 7YN2 Crystal structure of CcbD with methylthiolincosamide 2022-07-29 2023-08-02 Mori, T.,Lyu, S.,Abe, I. Crystal structure of CcbD with methylthiolincosamide To Be Published 0 0 0 0 7YN3 Crystal structure of CcbD complex with CcbZ carrier protein domain 2022-07-29 2023-08-02 Mori, T.,Lyu, S.,Abe, I. Crystal structure of CcbD complex with carrier protein To Be Published 0 0 0 0 8HB5 37521780 Crystal structure of Mincle in complex with HD-275 2022-10-27 2023-08-09 Ishizuka, S.,van Dijk, J.H.M.,Kawakita, T.,Miyamoto, Y.,Maeda, Y.,Goto, M.,Le Calvez, G.,Groot, L.M.,Witte, M.D.,Minnaard, A.J.,van der Marel, G.A.,Ato, M.,Nagae, M.,Codee, J.D.C.,Yamasaki, S. PGL-III, a Rare Intermediate of Mycobacterium leprae Phenolic Glycolipid Biosynthesis, Is a Potent Mincle Ligand. Acs Cent.Sci. 2023 9 1388 1399 8HRH 37547453 SN-131/1B2 anti-MUC1 antibody with a glycopeptide 2022-12-15 2023-08-30 Wakui, H.,Yokoi, Y.,Horidome, C.,Ose, T.,Yao, M.,Tanaka, Y.,Hinou, H.,Nishimura, S.I. Structural and molecular insight into antibody recognition of dynamic neoepitopes in membrane tethered MUC1 of pancreatic cancer cells and secreted exosomes. Rsc Chem Biol 2023 4 564 572 8W85 HLA-DQ2.5-gamma2 gliadin peptide in complex with DQN0385AE01 2023-08-31 2023-11-08 Okura, Y.,Ikawa-Teranishi, Y.,Mizoroki, A.,Takahashi, N.,Tsushima, T.,Irie, M.,Harfuddin, Z.,Miura-Okuda, M.,Ito, S.,Nakamura, G.,Takesue, H.,Ozono, Y.,Nishihara, M.,Yamada, K.,Gan, S.W.,Hayasaka, A.,Ishii, S.,Wakabayashi, T.,Muraoka, M.,Nagaya, N.,Hino, H.,Nemoto, T.,Kuramochi, T.,Torizawa, T.,Shimada, H.,Kitazawa, T.,Okazaki, M.,Nezu, J.,Sollid, L.M.,Igawa, T. Characterizations of a neutralizing antibody broadly reactive to multiple gluten peptide:HLA-DQ2.5 complexes in the context of celiac disease Nat Commun 2023 14 8502 0 8IN1 37910430 beta-glucosidase protein from Aplysia kurodai 2023-03-08 2023-11-15 Sun, X.,Ye, Y.,Sakurai, N.,Wang, H.,Kato, K.,Yu, J.,Yuasa, K.,Tsuji, A.,Yao, M. Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity. Elife 2023 12 0 0 8IN6 37910430 Eisenia hydrolysis-enhancing protein from Aplysia kurodai complex with tannic acid 2023-03-08 2023-11-15 Sun, X.,Ye, Y.,Sakurai, N.,Wang, H.,Kato, K.,Yu, J.,Yuasa, K.,Tsuji, A.,Yao, M. Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity. Elife 2023 12 0 0 8K6T 37994962 The minor pilin structure of FctB3 in Streptococcus 2023-07-25 2023-12-06 Takebe, K.,Suzuki, M.,Sangawa, T.,Kreikemeyer, B.,Yamaguchi, M.,Uzawa, N.,Sumitomo, T.,Kawabata, S.,Nakata, M. Analysis of FctB3 crystal structure and insight into its structural stabilization and pilin linkage mechanisms. Arch.Microbiol. 2023 206 4 4 8JMQ 37729620 Crystal structure of hinokiresinol synthase 2023-06-05 2023-12-20 Ushimaru, R.,Ding, Y.,Mori, T.,Miyamoto, K.,Uchiyama, M.,Abe, I. Structural and Mechanistic Insights into the C-C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase. J.Am.Chem.Soc. 2023 145 21966 21973 8JMR 37729620 Crystal structure of hinokiresinol synthase in complex with 1,7-bis(4-hydroxyphenyl)hepta-1,6-dien-3-one 2023-06-05 2023-12-20 Ushimaru, R.,Ding, Y.,Mori, T.,Miyamoto, K.,Uchiyama, M.,Abe, I. Structural and Mechanistic Insights into the C-C Bond-Forming Rearrangement Reaction Catalyzed by Heterodimeric Hinokiresinol Synthase. J.Am.Chem.Soc. 2023 145 21966 21973 8HVB Crystal structure of lacto-N-biosidase StrLNBase from Streptomyces sp. strain 142, lacto-N-biose complex 2022-12-26 2023-12-27 Fujio, N.,Yamada, C.,Fushinobu, S. Crystal structure of glycoside hydrolase family 20 lacto-N-biosidase from soil bacterium Streptomyces sp. strain 142 to be published 0 0 0 0 8HM9 X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 2022-12-02 2024-01-31 Aoyama, Y.,Yamaguchi, T.,Kohzuma, T. X-ray Crystal Structure of Pseudoazurin Met16His Variant at pH 4.0 To Be Published 0 0 0 0 8I56 CfbA S11T variant 2023-01-24 2024-01-31 Ogawa, S.,Hikita, M.,Fujishiro, T. Substrate selectivity of CfbA To be published 0 0 0 0 8XJ0 38295648 Crystal structure of AmFab mutant - P40C/E165C (Light chain), G10C/P210C(Heavy chain) 2023-12-20 2024-02-14 Yoshikawa, M.,Senda, M.,Nakamura, H.,Oda-Ueda, N.,Ueda, T.,Senda, T.,Ohkuri, T. Stabilization of adalimumab Fab through the introduction of disulfide bonds between the variable and constant domains. Biochem.Biophys.Res.Commun. 2024 700 149592 149592 8XHR Crystal structure of Mycobacterium tuberculosis MenT3 bound with CTP 2023-12-18 2024-02-28 Liu, J.,Yashiro, Y.,Sakaguchi, Y.,Suzuki, T.,Tomita, K. Substrate specificity of Mycobacterium tuberculosis terminal nucleotidyltransferase toxin MenT3 To Be Published 0 0 0 0 8IX6 Crystal structure of Pyruvic Oxime Dioxygenase (POD) from Bradyrhizobium sp. WSM3983 2023-03-31 2024-04-03 Tsujino, S.,Yamada, Y.,Senda, M.,Senda, T.,Fujiwara, T. Structural and functional analysis of pyruvic oxime dioxygenase, a key enzyme of heterotrophic nitrification To Be Published 0 0 0 0 8IXP Apo structure of glycosyltransferase LmbT wild type 2023-04-02 2024-04-03 Mori, T.,Sun, X.,Abe, I. Apo structure of glycosyltransferase LmbT wild type To Be Published 0 0 0 0 8IXQ Structure of glycosyltransferase LmbT in complex with GDP and ergothioneine 2023-04-02 2024-04-03 Mori, T.,Sun, X.,Abe, I. Structure of glycosyltransferase LmbT in complex with GDP and ergothioneine To Be Published 0 0 0 0 8J5E Crystal structure of kinase AbmG in complex with 4'-thiocytidine 2023-04-22 2024-04-24 Ushimaru, R.,Mori, T.,Liu, H.-w.,Abe, I. Crystal structure of kinase AbmG in complex with 4'-thiocytidine To Be Published 0 0 0 0 8J5F Crystal structure of kinase AbmG in complex with cytidine and ADP 2023-04-22 2024-04-24 Ushimaru, R.,Mori, T.,Liu, H.-w.,Abe, I. Crystal structure of kinase AbmG in complex with cytidine and ADP To Be Published 0 0 0 0 8J5G Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate 2023-04-22 2024-04-24 Ushimaru, R.,Mori, T.,Liu, H.-w.,Abe, I. Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 5'-diphosphate To Be Published 0 0 0 0 8J5H Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine 2023-04-22 2024-04-24 Ushimaru, R.,Mori, T.,Liu, H.-w.,Abe, I. Crystal structure of kinase AbmG in complex with 4'-hydroxy-4'-thiocytidine To Be Published 0 0 0 0