1VBM | | CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI TYROSYL-TRNA SYNTHETASE COMPLEXED WITH TYR-AMS | | Descriptor: | Tyrosyl-tRNA synthetase, SULFATE ION, 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE | | Authors: | Kobayashi, T., Sakamoto, K., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-02-27 | | Release date: | 2005-01-25 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
J.Mol.Biol., 346, 2005
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1VBN | | ESCHERICHIA COLI TYROSYL-TRNA SYNTHETASE MUTANT COMPLEXED WITH TYR-AMS | | Descriptor: | Tyrosyl-tRNA synthetase, 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE | | Authors: | Kobayashi, T., Sakamoto, K., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-02-27 | | Release date: | 2005-01-25 | | Last modified: | 2016-09-28 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1WQ3 | | ESCHERICHIA COLI TYROSYL-TRNA SYNTHETASE MUTANT COMPLEXED WITH 3-IODO-L-TYROSINE | | Descriptor: | Tyrosyl-tRNA synthetase, 3-IODO-TYROSINE | | Authors: | Kobayashi, T., Sakamoto, K., Nureki, O., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-20 | | Release date: | 2005-01-25 | | Last modified: | 2016-12-21 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1WQ4 | | ESCHERICHIA COLI TYROSYL-TRNA SYNTHETASE MUTANT COMPLEXED WITH L-TYROSINE | | Descriptor: | Tyrosyl-tRNA synthetase, TYROSINE | | Authors: | Kobayashi, T., Sakamoto, K., Nureki, O., Takimura, T., Kamata, K., Sekine, R., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-09-20 | | Release date: | 2005-01-25 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102, 2005
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1X8X | | TYROSYL T-RNA SYNTHETASE FROM E.COLI COMPLEXED WITH TYROSINE | | Descriptor: | Tyrosyl-tRNA synthetase, SULFATE ION, TYROSINE | | Authors: | Kobayashi, T., Takimura, T., Sekine, R., Kelly, V.P., Kamata, K., Sakamoto, K., Nishimura, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-08-19 | | Release date: | 2005-01-25 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural Snapshots of the KMSKS Loop Rearrangement for Amino Acid Activation by Bacterial Tyrosyl-tRNA Synthetase
J.MOL.BIOL., 346, 2005
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1J1U | | CRYSTAL STRUCTURE OF ARCHAEAL TYROSYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(TYR) AND L-TYROSINE | | Descriptor: | tRNA(Tyr), Tyrosyl-tRNA synthetase, MAGNESIUM ION, ... | | Authors: | Kobayashi, T., Nureki, O., Ishitani, R., Tukalo, M., Cusack, S., Sakamoto, K., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2002-12-17 | | Release date: | 2003-06-03 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion
NAT.STRUCT.BIOL., 10, 2003
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3VG9 | | CRYSTAL STRUCTURE OF HUMAN ADENOSINE A2A RECEPTOR WITH AN ALLOSTERIC INVERSE-AGONIST ANTIBODY AT 2.7 A RESOLUTION | | Descriptor: | Adenosine receptor A2a, antibody fab fragment light chain, antibody fab fragment heavy chain, ... | | Authors: | Hino, T., Arakawa, T., Iwanari, H., Yurugi-Kobayashi, T., Ikeda-Suno, C., Nakada-Nakura, Y., Kusano-Arai, O., Weyand, S., Shimamura, T., Nomura, N., Cameron, A.D., Kobayashi, T., Hamakubo, T., Iwata, S., Murata, T. | | Deposit date: | 2011-08-04 | | Release date: | 2012-02-01 | | Last modified: | 2012-02-15 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody
Nature, 482, 2012
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3VGA | | CRYSTAL STRUCTURE OF HUMAN ADENOSINE A2A RECEPTOR WITH AN ALLOSTERIC INVERSE-AGONIST ANTIBODY AT 3.1 A RESOLUTION | | Descriptor: | Adenosine receptor A2a, antibody fab fragment light chain, antibody fab fragment heavy chain, ... | | Authors: | Hino, T., Arakawa, T., Iwanari, H., Yurugi-Kobayashi, T., Ikeda-Suno, C., Nakada-Nakura, Y., Kusano-Arai, O., Weyand, S., Shimamura, T., Nomura, N., Cameron, A.D., Kobayashi, T., Hamakubo, T., Iwata, S., Murata, T. | | Deposit date: | 2011-08-04 | | Release date: | 2012-02-01 | | Last modified: | 2012-02-15 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody
Nature, 482, 2012
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5A16 | | CRYSTAL STRUCTURE OF FAB4201 RAISED AGAINST HUMAN ERYTHROCYTE ANION EXCHANGER 1 | | Descriptor: | FAB4201 HEAVY CHAIN | | Authors: | Arakawa, T., Kobayashi-Yugiri, T., Alguel, Y., Weyand, S., Iwanari, H., Hatae, H., Iwata, M., Abe, Y., Hino, T., Ikeda-Suno, C., Kuma, H., Kang, D., Murata, T., Hamakubo, T., Cameron, A., Kobayashi, T., Hamasaki, N., Iwata, S. | | Deposit date: | 2015-04-28 | | Release date: | 2015-06-10 | | Last modified: | 2019-10-23 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Crystal Structure of the Anion Exchanger Domain of Human Erythrocyte Band 3
Science, 350, 2015
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3UON | | STRUCTURE OF THE HUMAN M2 MUSCARINIC ACETYLCHOLINE RECEPTOR BOUND TO AN ANTAGONIST | | Descriptor: | Human M2 muscarinic acetylcholine, receptor T4 lysozyme fusion protein, (3R)-1-azabicyclo[2.2.2]oct-3-yl hydroxy(diphenyl)acetate, ... | | Authors: | Haga, K., Kruse, A.C., Asada, H., Yurugi-Kobayashi, T., Shiroishi, M., Zhang, C., Weis, W.I., Okada, T., Kobilka, B.K., Haga, T., Kobayashi, T. | | Deposit date: | 2011-11-16 | | Release date: | 2012-02-01 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist.
Nature, 482, 2012
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5H0Q | | CRYSTAL STRUCTURE OF LIPID BINDING PROTEIN NAKANORI AT 1.5A | | Descriptor: | Lipid binding protein | | Authors: | Makino, A., Abe, M., Ishitsuka, R., Murate, M., Kishimoto, T., Sakai, S., Hullin-Matsuda, F., Shimada, Y., Inaba, T., Miyatake, H., Tanaka, H., Kurahashi, A., Pack, C.G., Kasai, R.S., Kubo, S., Schieber, N.L., Dohmae, N., Tochio, N., Hagiwara, K., Sasaki, Y., Aida, Y., Fujimori, F., Kigawa, T., Nishikori, K., Parton, R.G., Kusumi, A., Sako, Y., Anderluh, G., Yamashita, M., Kobayashi, T., Greimel, P., Kobayashi, T. | | Deposit date: | 2016-10-06 | | Release date: | 2016-10-19 | | Last modified: | 2017-08-16 | | Method: | X-RAY DIFFRACTION (1.501 Å) | | Cite: | A novel sphingomyelin/cholesterol domain-specific probe reveals the dynamics of the membrane domains during virus release and in Niemann-Pick type C
FASEB J., 31, 2017
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4YZF | | CRYSTAL STRUCTURE OF THE ANION EXCHANGER DOMAIN OF HUMAN ERYTHROCYTE BAND 3 | | Descriptor: | Band 3 anion transport protein, FAB fragment of Immunoglobulin (IgG) molecule, 2,2'-ethane-1,2-diylbis{5-[(sulfanylmethyl)amino]benzenesulfonic acid} | | Authors: | Alguel, Y., Arakawa, T., Yugiri, T.K., Iwanari, H., Hatae, H., Iwata, M., Abe, Y., Hino, T., Suno, C.I., Kuma, H., Kang, D., Murata, T., Hamakubo, T., Cameron, A.D., Kobayashi, T., Hamasaki, N., Iwata, S. | | Deposit date: | 2015-03-25 | | Release date: | 2015-11-04 | | Last modified: | 2015-11-18 | | Method: | X-RAY DIFFRACTION (3.5 Å) | | Cite: | Crystal structure of the anion exchanger domain of human erythrocyte band 3.
Science, 350, 2015
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1WSD | | ALKALINE M-PROTEASE FORM I CRYSTAL STRUCTURE | | Descriptor: | M-protease, CALCIUM ION, SULFATE ION | | Authors: | Shirai, T., Suzuki, A., Yamane, T., Ashida, T., Kobayashi, T., Hitomi, J., Ito, S. | | Deposit date: | 2004-11-05 | | Release date: | 2004-11-16 | | Last modified: | 2020-09-09 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism
Protein Eng., 10, 1997
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4X8Y | | CRYSTAL STRUCTURE OF HUMAN PGRMC1 CYTOCHROME B5-LIKE DOMAIN | | Descriptor: | Membrane-associated progesterone receptor component 1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nakane, T., Yamamoto, T., Shimamura, T., Kobayashi, T., Kabe, Y., Suematsu, M. | | Deposit date: | 2014-12-11 | | Release date: | 2016-03-23 | | Last modified: | 2020-02-05 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Haem-dependent dimerization of PGRMC1/Sigma-2 receptor facilitates cancer proliferation and chemoresistance
Nat Commun, 7, 2016
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5WQC | | CRYSTAL STRUCTURE OF HUMAN OREXIN 2 RECEPTOR BOUND TO THE SELECTIVE ANTAGONIST EMPA DETERMINED BY THE SYNCHROTRON LIGHT SOURCE AT SPRING-8. | | Descriptor: | Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, ... | | Authors: | Suno, R., Hirata, K., Yamashita, K., Tsujimoto, H., Sasanuma, M., Horita, S., Yamamoto, M., Rosenbaum, D.M., Iwata, S., Shimamura, T., Kobayashi, T. | | Deposit date: | 2016-11-25 | | Release date: | 2017-11-29 | | Last modified: | 2018-01-17 | | Method: | X-RAY DIFFRACTION (1.96 Å) | | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA
Structure, 26, 2018
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5WS3 | | CRYSTAL STRUCTURES OF HUMAN OREXIN 2 RECEPTOR BOUND TO THE SELECTIVE ANTAGONIST EMPA DETERMINED BY SERIAL FEMTOSECOND CRYSTALLOGRAPHY AT SACLA | | Descriptor: | Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2, N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl)sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide, OLEIC ACID, ... | | Authors: | Suno, R., Kimura, K., Nakane, T., Yamashita, K., Wang, J., Fujiwara, T., Yamanaka, Y., Im, D., Tsujimoto, H., Sasanuma, M., Horita, S., Hirokawa, T., Nango, E., Tono, K., Kameshima, T., Hatsui, T., Joti, Y., Yabashi, M., Shimamoto, K., Yamamoto, M., Rosenbaum, D.M., Iwata, S., Shimamura, T., Kobayashi, T. | | Deposit date: | 2016-12-05 | | Release date: | 2017-12-13 | | Last modified: | 2018-06-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.
Structure, 26, 2018
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5YFI | | CRYSTAL STRUCTURE OF THE ANTI-HUMAN PROSTAGLANDIN E RECEPTOR EP4 ANTIBODY FAB FRAGMENT | | Descriptor: | Light chain of Fab fragment, Heavy chain of Fab fragment, ZINC ION | | Authors: | Toyoda, Y., Morimoto, K., Suno, R., Horita, S., Iwata, S., Kobayashi, T. | | Deposit date: | 2017-09-21 | | Release date: | 2018-12-05 | | Last modified: | 2019-03-06 | | Method: | X-RAY DIFFRACTION (1.848 Å) | | Cite: | Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.
Nat. Chem. Biol., 15, 2019
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5YHL | | CRYSTAL STRUCTURE OF THE HUMAN PROSTAGLANDIN E RECEPTOR EP4 IN COMPLEX WITH FAB AND AN ANTAGONIST BR-DERIVATIVE | | Descriptor: | Prostaglandin E2 receptor EP4 subtype, Heavy chain of Fab fragment, Light chain of Fab fragment, ... | | Authors: | Toyoda, Y., Morimoto, K., Suno, R., Horita, S., Iwata, S., Kobayashi, T. | | Deposit date: | 2017-09-28 | | Release date: | 2018-12-05 | | Last modified: | 2019-01-30 | | Method: | X-RAY DIFFRACTION (4.2 Å) | | Cite: | Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.
Nat. Chem. Biol., 15, 2019
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5YWY | | CRYSTAL STRUCTURE OF THE HUMAN PROSTAGLANDIN E RECEPTOR EP4 IN COMPLEX WITH FAB AND ONO-AE3-208 | | Descriptor: | Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype, Heavy chain of Fab fragment, Light chain of Fab fragment, ... | | Authors: | Toyoda, Y., Morimoto, K., Suno, R., Horita, S., Iwata, S., Kobayashi, T. | | Deposit date: | 2017-11-30 | | Release date: | 2018-12-05 | | Last modified: | 2018-12-19 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Ligand binding to human prostaglandin E receptor EP4at the lipid-bilayer interface.
Nat. Chem. Biol., 15, 2019
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2CYA | | CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE FROM AEROPYRUM PERNIX | | Descriptor: | Tyrosyl-tRNA synthetase, SULFATE ION | | Authors: | Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Kuroishi, C., Kuramitsu, S., Terada, T., Bessho, Y., Shirouzu, M., Sekine, S.I., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-06 | | Release date: | 2005-11-22 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
J.Mol.Biol., 355, 2005
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2CYB | | CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE COMPLEXED WITH L-TYROSINE FROM ARCHAEOGLOBUS FULGIDUS | | Descriptor: | Tyrosyl-tRNA synthetase, TYROSINE | | Authors: | Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-06 | | Release date: | 2005-11-22 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
J.Mol.Biol., 355, 2006
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2CYC | | CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE COMPLEXED WITH L-TYROSINE FROM PYROCOCCUS HORIKOSHII | | Descriptor: | tyrosyl-tRNA synthetase, TYROSINE | | Authors: | Kuratani, M., Sakai, H., Takahashi, M., Yanagisawa, T., Kobayashi, T., Sakamoto, K., Terada, T., Shirouzu, M., Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2005-07-06 | | Release date: | 2005-11-22 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal Structures of Tyrosyl-tRNA Synthetases from Archaea
J.Mol.Biol., 355, 2006
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2DIE | | ALKALINE ALPHA-AMYLASE AMYK FROM BACILLUS SP. KSM-1378 | | Descriptor: | amylase, CALCIUM ION, SODIUM ION | | Authors: | Shirai, T., Igarashi, K., Ozawa, T., Hagihara, H., Kobayashi, T., Ozaki, K., Ito, S. | | Deposit date: | 2006-03-29 | | Release date: | 2007-02-13 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins
Proteins, 66, 2007
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1EE6 | | CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15. | | Descriptor: | PECTATE LYASE, CALCIUM ION | | Authors: | Akita, M., Suzuki, A., Kobayashi, T., Ito, S., Yamane, T. | | Deposit date: | 2000-01-31 | | Release date: | 2001-01-31 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The first structure of pectate lyase belonging to polysaccharide lyase family 3.
Acta Crystallogr.,Sect.D, 57, 2001
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2ZE0 | | ALPHA-GLUCOSIDASE GSJ | | Descriptor: | Alpha-glucosidase, CALCIUM ION | | Authors: | Shirai, T., Hung, V.S., Morinaka, K., Kobayashi, T., Ito, S. | | Deposit date: | 2007-12-04 | | Release date: | 2007-12-18 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria
Proteins, 73, 2008
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