PDB_ID PUBMED_CID STRUCTURE TITLE DEPOSITION DATE RELEASE DATE AUTHORS CITATION TITLE JOURNAL YEAR VOLUME FIRST PAGE LAST PAGE 1IT7 12054814 Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine 2002-01-11 2002-05-22 Ishitani, R.,Nureki, O.,Fukai, S.,Kijimoto, T.,Nameki, N.,Watanabe, M.,Kondo, H.,Sekine, M.,Okada, N.,Nishimura, S.,Yokoyama, S. Crystal structure of archaeosine tRNA-guanine transglycosylase. J.Mol.Biol. 2002 318 665 677 1IT8 12054814 Crystal structure of archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii complexed with archaeosine precursor, preQ0 2002-01-11 2002-05-22 Ishitani, R.,Nureki, O.,Fukai, S.,Kijimoto, T.,Nameki, N.,Watanabe, M.,Kondo, H.,Sekine, M.,Okada, N.,Nishimura, S.,Yokoyama, S. Crystal structure of archaeosine tRNA-guanine transglycosylase. J.Mol.Biol. 2002 318 665 677 1IW7 12000971 Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution 2002-04-22 2002-06-26 Vassylyev, D.G.,Sekine, S.,Laptenko, O.,Lee, J.,Vassylyeva, M.N.,Borukhov, S.,Yokoyama, S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution NATURE 2002 417 712 719 1KN0 12191481 Crystal Structure of the human Rad52 protein 2001-12-18 2002-09-04 Kagawa, W.,Kurumizaka, H.,Ishitani, R.,Fukai, S.,Nureki, O.,Shibata, T.,Yokoyama, S. Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Mol.Cell 2002 10 359 371 1IWQ 12577052 Crystal Structure of MARCKS calmodulin binding domain peptide complexed with Ca2+/Calmodulin 2002-05-31 2003-03-11 Yamauchi, E.,Nakatsu, T.,Matsubara, M.,Kato, H.,Taniguchi, H. Crystal structure of a MARCKS peptide containing the calmodulin-binding domain in complex with Ca(2+)-calmodulin NAT.STRUCT.BIOL. 2003 10 226 231 1IW1 14645223 Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferrous state 2002-04-04 2003-04-04 Hirotsu, S.,Chu, G.C.,Unno, M.,Lee, D.S.,Yoshida, T.,Park, S.Y.,Shiro, Y.,Ikeda-Saito, M. The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae. J.Biol.Chem. 2004 279 11937 11947 1IW0 14645223 Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed with heme in the ferric state 2002-04-04 2003-04-08 Hirotsu, S.,Chu, G.C.,Unno, M.,Lee, D.S.,Yoshida, T.,Park, S.Y.,Shiro, Y.,Ikeda-Saito, M. The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae. J.Biol.Chem. 2004 279 11937 11947 1IZN 12660160 Crystal Structure of Actin Filament Capping Protein CapZ 2002-10-10 2003-04-08 Yamashita, A.,Maeda, K.,Maeda, Y. Crystal structure of CapZ: structural basis for actin filament barbed end capping EMBO J. 2003 22 1529 1538 1K1W 12618437 Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis 2001-09-26 2003-06-17 Imamura, H.,Fushinobu, S.,Yamamoto, M.,Kumasaka, T.,Jeon, B.S.,Wakagi, T.,Matsuzawa, H. Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor J.BIOL.CHEM. 2003 278 19378 19386 1K1X 12618437 Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis 2001-09-26 2003-06-17 Imamura, H.,Fushinobu, S.,Yamamoto, M.,Kumasaka, T.,Jeon, B.S.,Wakagi, T.,Matsuzawa, H. Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor J.BIOL.CHEM. 2003 278 19378 19386 1UD2 12719434 Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) 2003-04-28 2003-07-22 Nonaka, T.,Fujihashi, M.,Kita, A.,Hagihara, H.,Ozaki, K.,Ito, S.,Miki, K. Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites J.Biol.Chem. 2003 278 24818 24824 1UD3 12719434 Crystal structure of AmyK38 N289H mutant 2003-04-28 2003-07-22 Nonaka, T.,Fujihashi, M.,Kita, A.,Hagihara, H.,Ozaki, K.,Ito, S.,Miki, K. Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites J.Biol.Chem. 2003 278 24818 24824 1IXL 14997554 Crystal structure of uncharacterized protein PH1136 from Pyrococcus horikoshii 2002-06-27 2003-09-09 Tajika, Y.,Sakai, N.,Tanaka, Y.,Yao, M.,Watanabe, N.,Tanaka, I. Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii. Proteins 2004 55 210 213 1L7Z 14765114 Crystal structure of Ca2+/Calmodulin complexed with myristoylated CAP-23/NAP-22 peptide 2002-03-18 2003-09-16 Matsubara, M.,Nakatsu, T.,Kato, H.,Taniguchi, H. Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin EMBO J. 2004 23 712 718 1UC8 12963379 Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8 2003-04-09 2003-09-23 Sakai, H.,Vassylyeva, M.N.,Matsuura, T.,Sekine, S.,Gotoh, K.,Nishiyama, M.,Terada, T.,Shirouzu, M.,Kuramitsu, S.,Vassylyev, D.G.,Yokoyama, S. Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8 J.Mol.Biol. 2003 332 729 740 1UFR Crystal Structure of TT1027 from Thermus thermophilus HB8 2003-06-08 2003-12-08 Matsuura, T.,Sakai, H.,Terada, T.,Shirouzu, M.,Kuramitsu, S.,Yokoyama, S. Crystal Structure of TT1027 from Thermus thermophilus HB8 To be Published 0 0 0 0 1Q3S 14729342 Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP) 2003-07-31 2004-01-27 Shomura, Y.,Yoshida, T.,Iizuka, R.,Maruyama, T.,Yohda, M.,Miki, K. Crystal Structures of the Group II Chaperonin from Thermococcus strain KS-1: Steric Hindrance by the Substituted Amino Acid, and Inter-subunit Rearrangement between Two Crystal Forms. J.Mol.Biol. 2004 335 1265 1278 1J1Y 16061252 Crystal Structure of PaaI from Thermus thermophilus HB8 2002-12-24 2004-02-17 Kunishima, N.,Asada, Y.,Sugahara, M.,Ishijima, J.,Nodake, Y.,Sugahara, M.,Miyano, M.,Kuramitsu, S.,Yokoyama, S.,Sugahara, M. A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI J.Mol.Biol. 2005 352 212 228 1SMY 15109491 Structural basis for transcription regulation by alarmone ppGpp 2004-03-10 2004-05-18 Artsimovitch, I.,Patlan, V.,Sekine, S.,Vassylyeva, M.N.,Hosaka, T.,Ochi, K.,Yokoyama, S.,Vassylyev, D.G. Structural basis for transcription regulation by alarmone ppGpp Cell(Cambridge,Mass.) 2004 117 299 310 1UEB 15210970 Crystal structure of translation elongation factor P from Thermus thermophilus HB8 2003-05-09 2004-05-25 Hanawa-Suetsugu, K.,Sekine, S.,Sakai, H.,Hori-Takemoto, C.,Terada, T.,Unzai, S.,Tame, J.R.H.,Kuramitsu, S.,Shirouzu, M.,Yokoyama, S. Crystal structure of elongation factor P from Thermus thermophilus HB8 Proc.Natl.Acad.Sci.USA 2004 101 9595 9600 1VFJ 15629661 Crystal structure of TT1020 from Thermus thermophilus HB8 2004-04-15 2005-01-11 Sakai, H.,Wang, H.,Takemoto-Hori, C.,Kaminishi, T.,Yamaguchi, H.,Kamewari, Y.,Terada, T.,Kuramitsu, S.,Shirouzu, M.,Yokoyama, S. Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8 J.STRUCT.BIOL. 2005 149 99 110 1V8E Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase from Thermus thermophilus HB8 2004-01-05 2005-01-18 Ishijima, J.,Ida, K.,Yutani, K.,Miyano, M. Crystal structure of glycerophosphoryl diester phosphodiesterase from Thermus thermophilus HB8 To be Published 0 0 0 0 1WXR 15728184 Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli 2005-01-31 2005-03-01 Otto, B.R.,Sijbrandi, R.,Luirink, J.,Oudega, B.,Heddle, J.G.,Mizutani, K.,Park, S.-Y.,Tame, J.R.H. Crystal structure of heme binding protein, an autotransporter hemoglobin protease from pathogenic escherichia coli J.Biol.Chem. 2005 280 17339 17345 1VBH 15667207 Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize 2004-02-26 2005-03-08 Nakanishi, T.,Nakatsu, T.,Matsuoka, M.,Sakata, K.,Kato, H. Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion Biochemistry 2005 44 1136 1144 1WDT Crystal structure of ttk003000868 from Thermus thermophilus HB8 2004-05-17 2005-05-17 Wang, H.,Takemoto-Hori, C.,Murayama, K.,Sekine, S.,Terada, T.,Shirouzu, M.,Kuramitsu, S.,Yokoyama, S. Crystal structure of ttk003000868 from Thermus thermophilus HB8 To be published 0 0 0 0 1WM6 16061252 Crystal structure of TT0310 protein from Thermus thermophilus HB8 2004-07-04 2005-07-05 Kunishima, N.,Asada, Y.,Sugahara, M.,Ishijima, J.,Nodake, Y.,Sugahara, M.,Miyano, M.,Kuramitsu, S.,Yokoyama, S.,Sugahara, M. A Novel Induced-fit Reaction Mechanism of Asymmetric Hot Dog Thioesterase PaaI J.Mol.Biol. 2005 352 212 228 1WM9 16169877 Structure of GTP cyclohydrolase I from Thermus thermophilus HB8 2004-07-05 2005-07-19 Tanaka, Y.,Nakagawa, N.,Kuramitsu, S.,Yokoyama, S.,Masui, R. Novel Reaction Mechanism of GTP Cyclohydrolase I. High-Resolution X-Ray Crystallography of Thermus thermophilus HB8 Enzyme Complexed with a Transition State Analogue, the 8-Oxoguanine Derivative. J.Biochem.(Tokyo) 2005 138 263 275 2COV 16061225 Crystal structure of CBM31 from beta-1,3-xylanase 2005-05-18 2005-09-13 Hashimoto, H.,Tamai, Y.,Okazaki, F.,Tamaru, Y.,Shimizu, T.,Araki, T.,Sato, M. The first crystal structure of a family 31 carbohydrate-binding module with affinity to beta-1,3-xylan Febs Lett. 2005 579 4324 4328 1WRV Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase 2004-10-27 2005-10-18 Goto, M.,Miyahara, I.,Hirotsu, K. Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase TO BE PUBLISHED 0 0 0 0 1WRK Crystal structure of the N-terminal domain of human cardiac troponin C in complex with trifluoperazine (orthrombic crystal form) 2004-10-20 2006-01-24 Takeda, S.,Igarashi, T.,Oishi, Y.,Mori, H. Crystal structure of the N-terminal domain of human cardiac troponin C in complex with trifluoperazine To be Published 0 0 0 0 1WRL Crystal structure of the N-terminal domain of human cardiac troponin C in complex with trifluoperazine (monoclinic crystal form) 2004-10-20 2006-01-24 Takeda, S.,Igarashi, T.,Oishi, Y.,Mori, H. Crystal structure of the N-terminal domain of human cardiac troponin C in complex with trifluoperazine To be Published 0 0 0 0 1X03 16763557 Crystal structure of endophilin BAR domain 2005-03-14 2006-05-02 Masuda, M.,Takeda, S.,Sone, M.,Ohki, T.,Mori, H.,Kamioka, Y.,Mochizuki, N. Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms Embo J. 2006 25 2889 2897 1X04 16763557 Crystal structure of endophilin BAR domain (mutant) 2005-03-14 2006-05-02 Masuda, M.,Takeda, S.,Sone, M.,Ohki, T.,Mori, H.,Kamioka, Y.,Mochizuki, N. Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms Embo J. 2006 25 2889 2897 2DC3 16699195 Crystal structure of human cytoglobin at 1.68 angstroms resolution 2005-12-21 2006-05-23 Makino, M.,Sugimoto, H.,Sawai, H.,Kawada, N.,Yoshizato, K.,Shiro, Y. High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode. Acta Crystallogr.,Sect.D 2006 62 671 677 2ERO 16688218 Crystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form) 2005-10-25 2006-06-20 Takeda, S.,Igarashi, T.,Mori, H.,Araki, S. Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold Embo J. 2006 25 2388 2396 2ERQ 16688218 Crystal structure of vascular apoptosis-inducing protein-1(tetragonal crystal form) 2005-10-25 2006-06-20 Takeda, S.,Igarashi, T.,Mori, H.,Araki, S. Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold Embo J. 2006 25 2388 2396 2PCJ Crystal structure of ABC transporter (aq_297) From Aquifex Aeolicus VF5 2007-03-30 2007-10-02 Jeyakanthan, J.,Kanaujia, S.P.,Vasuki Ranjani, C.,Sekar, K.,Nakagawa, N.,Ebihara, A.,Kuramitsu, S.,Shinkai, A.,Shiro, Y.,Yokoyama, S. Crystal structure of ABC transporter (aq_297) From Aquifex Aeolicus VF5 To be Published 0 0 0 0 2PCN Crystal structure of S-adenosylmethionine: 2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426 2007-03-30 2007-10-02 Jeyakanthan, J.,Kanaujia, S.P.,Rafi, Z.A.,Sekar, K.,Agari, Y.,Ebihara, A.,Kuramitsu, S.,Shinkai, A.,Shiro, Y.,Yokoyama, S. Crystal structure of S-adenosylmethionine:2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426 To be Published 0 0 0 0 2YW3 Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1 2007-04-19 2007-10-23 Kawano, Y.,Hashimoto, K.,Kamiya, N. Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1 To be published 0 0 0 0 2ZE5 18258747 Crystal Structure of adenosine phosphate-isopentenyltransferase 2007-12-06 2008-02-05 Sugawara, H.,Ueda, N.,Kojima, M.,Makita, N.,Yamaya, T.,Sakakibara, H. Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis. Proc.Natl.Acad.Sci.Usa 2008 105 2734 2739 2ZE6 18258747 Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with substrate analog, DMASPP 2007-12-06 2008-02-05 Sugawara, H.,Ueda, N.,Kojima, M.,Makita, N.,Yamaya, T.,Sakakibara, H. Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis. Proc.Natl.Acad.Sci.Usa 2008 105 2734 2739 2ZE7 18258747 Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with zinc ion and substrate analog, DMASPP 2007-12-06 2008-02-05 Sugawara, H.,Ueda, N.,Kojima, M.,Makita, N.,Yamaya, T.,Sakakibara, H. Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis. Proc.Natl.Acad.Sci.Usa 2008 105 2734 2739 2ZE8 18258747 Crystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate 2007-12-06 2008-02-05 Sugawara, H.,Ueda, N.,Kojima, M.,Makita, N.,Yamaya, T.,Sakakibara, H. Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis. Proc.Natl.Acad.Sci.Usa 2008 105 2734 2739 3CM0 Crystal structure of adenylate kinase from Thermus thermophilus HB8 2008-03-20 2008-09-23 Nakagawa, N.,Kondo, N.,Masui, R.,Yokoyama, S.,Kuramitsu, S. Crystal structure of adenylate kinase from Thermus thermophilus HB8. To be Published 0 0 0 0 3W8N Open form structure of CMP kinase in complex with CMP from Thermus thermophilus HB8 2013-03-19 2013-09-25 Mega, R.,Nakagawa, N.,Masui, R.,Kuramitsu, S. Crystal structure of CMP kinase: insights into initial substrate recognition and reaction mechanisms To be Published 0 0 0 0 3W90 Crystal structure of CMP kinase from Thermus thermophilus HB8 2013-03-22 2013-09-25 Mega, R.,Nakagawa, N.,Masui, R.,Kuramitsu, S. Crystal structure of CMP kinase: insights into initial substrate recognition and reaction mechanisms To be Published 0 0 0 0 4OIW 24704201 Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa 2014-01-20 2014-04-02 Nguyen, D.D.,Pandian, R.,Kim, D.,Ha, S.C.,Yoon, H.J.,Kim, K.S.,Yun, K.H.,Kim, J.H.,Kim, K.K. Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa Biochem.Biophys.Res.Commun. 2014 447 101 107 3WU1 25083921 Crystal structure of the ETS1-RUNX1-DNA ternary complex 2014-04-21 2014-08-20 Shiina, M.,Hamada, K.,Inoue-Bungo, T.,Shimamura, M.,Uchiyama, A.,Baba, S.,Sato, K.,Yamamoto, M.,Ogata, K. A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions. J.Mol.Biol. 2015 427 1655 1669 5TMC 25352397 Re-refinement of Thermus thermopiles DNA-directed RNA polymerase structure 2016-10-12 2016-11-23 Wang, J. On the validation of crystallographic symmetry and the quality of structures. Protein Sci. 2015 24 621 632 9DTY 40991405 Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB 2024-10-02 2025-10-01 Hulse, M.,Wang, M.,Xu, C.,Carter, J.,Agarwal, A.,Lu, L.,Pitis, P.,Bhagwat, N.,Rager, J.,Kurian, J.,Basch, C.,Sivakumar, M.,Burtell, J.,Mondal, A.,Grego, A.,Moore, A.,Bachner, C.,Vykuntam, K.,Reichelderfer, A.,Park, J.,Cote, J.,Cowart, M.,Osinubi, O.P.,Bigot, L.,Da Silva, A.,Nobre, C.,Meteau, M.,Soares, M.,Tang, H.Y.,Bersch, K.,Dai, C.,Cao, G.,Shen, B.,Emm, T.,Ruepp, S.,Xavier, J.,Tankersley, C.,Heiser, D.,Lee, S.H.,Geeganage, S.,Ruggeri, B.,Lin, H.,Novotny, W.,Huang, J.,Vaddi, K.,Combs, A.,Scherle, P.,Ito, K. PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers. Cancer Res. 2025 0 0 0