2DQU
 
 | | Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | | Descriptor: | IMMUNOGLOBULIN 6D9, [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER | | Authors: | Kristensen, O, Vassylyev, D.G, Tanaka, F, Ito, N, Morikawa, K, Fujii, I. | | Deposit date: | 2006-05-30 | | Release date: | 2006-06-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis
J.Mol.Biol., 369, 2007
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1H38
 | | Structure of a T7 RNA polymerase elongation complex at 2.9A resolution | | Descriptor: | 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3', 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3', 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3', ... | | Authors: | Tahirov, T.H, Temyakov, D, Anikin, M, Patlan, V, McAllister, W.T, Vassylyev, D.G, Yokoyama, S. | | Deposit date: | 2002-08-24 | | Release date: | 2002-11-20 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structure of a T7 RNA Polymerase Elongation Complex at 2.9 A Resolution
Nature, 420, 2002
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1VMO
 | | CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VMO-I): A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY STRUCTURES RELATED BY AN INTERNAL THREE-FOLD SYMMETRY | | Descriptor: | VITELLINE MEMBRANE OUTER LAYER PROTEIN I | | Authors: | Shimizu, T, Vassylyev, D.G, Kido, S, Doi, Y, Morikawa, K. | | Deposit date: | 1994-01-06 | | Release date: | 1994-05-31 | | Last modified: | 2024-06-05 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry.
EMBO J., 13, 1994
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1B70
 | | PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINE | | Descriptor: | MAGNESIUM ION, PHENYLALANINE, PHENYLALANYL-TRNA SYNTHETASE | | Authors: | Reshetnikova, L, Moor, N, Lavrik, O, Vassylyev, D.G. | | Deposit date: | 1999-01-26 | | Release date: | 2000-02-09 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue
J.Mol.Biol., 287, 1999
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1J09
 | | Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with ATP and Glu | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, GLUTAMIC ACID, Glutamyl-tRNA synthetase, ... | | Authors: | Sekine, S, Nureki, O, Dubois, D.Y, Bernier, S, Chenevert, R, Lapointe, J, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-11-12 | | Release date: | 2003-02-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
EMBO J., 22, 2003
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1B7Y
 | | PHENYLALANYL TRNA SYNTHETASE COMPLEXED WITH PHENYLALANINYL-ADENYLATE | | Descriptor: | ADENOSINE-5'-[PHENYLALANINOL-PHOSPHATE], MAGNESIUM ION, PROTEIN (PHENYLALANYL-TRNA SYNTHETASE) | | Authors: | Reshetnikova, L, Moor, N, Lavrik, O, Vassylyev, D.G. | | Deposit date: | 1999-01-26 | | Release date: | 2000-01-26 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.
J.Mol.Biol., 287, 1999
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2DQT
 | | High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog | | Descriptor: | IMMUNOGLOBULIN 6D9, [1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER | | Authors: | Kristensen, O, Vassylyev, D.G, Tanaka, F, Ito, N, Morikawa, K, Fujii, I. | | Deposit date: | 2006-05-30 | | Release date: | 2006-06-20 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis
J.Mol.Biol., 369, 2007
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1FL0
 | | CRYSTAL STRUCTURE OF THE EMAP2/RNA-BINDING DOMAIN OF THE P43 PROTEIN FROM HUMAN AMINOACYL-TRNA SYNTHETASE COMPLEX | | Descriptor: | ENDOTHELIAL-MONOCYTE ACTIVATING POLYPEPTIDE II | | Authors: | Renault, L, Kerjan, P, Pasqualato, S, Menetrey, J, Robinson, J.-C, Kawaguchi, S, Vassylyev, D.G, Yokoyama, S, Mirande, M, Cherfils, J. | | Deposit date: | 2000-08-11 | | Release date: | 2000-12-06 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.
EMBO J., 20, 2001
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1HJR
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1GLN
 | | ARCHITECTURES OF CLASS-DEFINING AND SPECIFIC DOMAINS OF GLUTAMYL-TRNA SYNTHETASE | | Descriptor: | GLUTAMYL-TRNA SYNTHETASE | | Authors: | Nureki, O, Vassylyev, D.G, Katayanagi, K, Shimizu, T, Sekine, S, Kigawa, T, Miyazawa, T, Yokoyama, S, Morikawa, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1994-07-20 | | Release date: | 1995-10-15 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
Science, 267, 1995
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1ILE
 | | ISOLEUCYL-TRNA SYNTHETASE | | Descriptor: | ISOLEUCYL-TRNA SYNTHETASE, ZINC ION | | Authors: | Nureki, O, Vassylyev, D.G, Tateno, M, Shimada, A, Nakama, T, Fukai, S, Konno, M, Schimmel, P, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1998-02-24 | | Release date: | 1999-04-13 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Enzyme structure with two catalytic sites for double-sieve selection of substrate.
Science, 280, 1998
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1IPA
 | | CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE | | Descriptor: | RNA 2'-O-RIBOSE METHYLTRANSFERASE | | Authors: | Nureki, O, Shirouzu, M, Hashimoto, K, Ishitani, R, Terada, T, Tamakoshi, M, Oshima, T, Chijimatsu, M, Takio, K, Vassylyev, D.G, Shibata, T, Inoue, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2001-05-02 | | Release date: | 2002-07-10 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | An enzyme with a deep trefoil knot for the active-site architecture.
Acta Crystallogr.,Sect.D, 58, 2002
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1GD7
 | | CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES. | | Descriptor: | CSAA PROTEIN | | Authors: | Shibata, T, Inoue, Y, Vassylyev, D.G, Kawaguchi, S, Yokoyama, S, Muller, J, Linde, D, Kuramitsu, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2000-09-22 | | Release date: | 2001-09-22 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
EMBO J., 20, 2001
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1FUT
 | | CRYSTAL STRUCTURES OF RIBONUCLEASE F1 OF FUSARIUM MONILIFORME IN ITS FREE FORM AND IN COMPLEX WITH 2'GMP | | Descriptor: | GUANOSINE-2'-MONOPHOSPHATE, RIBONUCLEASE F1 | | Authors: | Katayanagi, K, Vassylyev, D.G, Ishikawa, K, Morikawa, K. | | Deposit date: | 1993-01-18 | | Release date: | 1993-10-31 | | Last modified: | 2019-12-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structures of ribonuclease F1 of Fusarium moniliforme in its free form and in complex with 2'GMP.
J.Mol.Biol., 230, 1993
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1FUS
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1AT9
 | | STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY | | Descriptor: | BACTERIORHODOPSIN, RETINAL | | Authors: | Kimura, Y, Vassylyev, D.G, Miyazawa, A, Kidera, A, Matsushima, M, Mitsuoka, K, Murata, K, Hirai, T, Fujiyoshi, Y. | | Deposit date: | 1997-08-20 | | Release date: | 1998-09-16 | | Last modified: | 2024-06-05 | | Method: | ELECTRON CRYSTALLOGRAPHY (2.8 Å) | | Cite: | Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.
Nature, 389, 1997
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2ZJS
 | | Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment | | Descriptor: | Fab56 (heavy chain), Fab56 (light chain), Preprotein translocase SecE subunit, ... | | Authors: | Tsukazaki, T, Mori, H, Fukai, S, Ishitani, R, Perederina, A, Vassylyev, D.G, Ito, K, Nureki, O. | | Deposit date: | 2008-03-08 | | Release date: | 2008-10-14 | | Last modified: | 2021-11-10 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Conformational transition of Sec machinery inferred from bacterial SecYE structures
Nature, 455, 2008
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1IYW
 | | Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase | | Descriptor: | Valyl-tRNA Synthetase | | Authors: | Fukai, S, Nureki, O, Sekine, S, Shimada, A, Vassylyev, D.G, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-09-10 | | Release date: | 2003-06-17 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (4 Å) | | Cite: | Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9, 2003
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