5KND
 
 | | Crystal structure of the Pi-bound V1 complex | | Descriptor: | 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, GLYCEROL, MAGNESIUM ION, ... | | Authors: | Suzuki, K, Mizutani, K, Maruyama, S, Shimono, K, Imai, F.L, Muneyuki, E, Kakinuma, Y, Ishizuka-Katsura, Y, Shirouzu, M, Yokoyama, S, Yamato, I, Murata, T. | | Deposit date: | 2016-06-28 | | Release date: | 2016-11-02 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.888 Å) | | Cite: | Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor
Nat Commun, 7, 2016
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8KCQ
 | | Solution structures of the N-terminal divergent caplonin homology (NN-CH) domains of human intraflagellar transport protein 54 | | Descriptor: | TRAF3-interacting protein 1 | | Authors: | Dang, W, Kuwasako, K, He, F, Takahashi, M, Tsuda, K, Nagata, T, Tanaka, A, Kobayashi, N, Kigawa, T, Guentert, P, Shirouzu, M, Yokoyama, S, Muto, Y, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2023-08-08 | | Release date: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | 1 H, 13 C, and 15 N resonance assignments and solution structure of the N-terminal divergent calponin homology (NN-CH) domain of human intraflagellar transport protein 54.
Biomol.Nmr Assign., 18, 2024
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4YVG
 | | Crystal Structure of H. influenzae TrmD in complex with AdoMet | | Descriptor: | S-ADENOSYLMETHIONINE, tRNA (guanine-N(1)-)-methyltransferase | | Authors: | Ito, T, Yokoyama, S. | | Deposit date: | 2015-03-20 | | Release date: | 2015-07-15 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.549 Å) | | Cite: | Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
Proc.Natl.Acad.Sci.USA, 112, 2015
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4YVH
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4YVI
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4YVK
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4YVJ
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3NJP
 | | The Extracellular and Transmembrane Domain Interfaces in Epidermal Growth Factor Receptor Signaling | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Epidermal growth factor, Epidermal growth factor receptor, ... | | Authors: | Lu, C, Mi, L.-Z, Grey, M.J, Zhu, J, Graef, E, Yokoyama, S, Springer, T.A. | | Deposit date: | 2010-06-17 | | Release date: | 2010-10-13 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (3.304 Å) | | Cite: | Structural evidence for loose linkage between ligand binding and kinase activation in the epidermal growth factor receptor.
Mol.Cell.Biol., 30, 2010
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4LM5
 | | Crystal structure of Pim1 in complex with 2-{4-[(3-aminopropyl)amino]quinazolin-2-yl}phenol (resulting from displacement of SKF86002) | | Descriptor: | 2-{4-[(3-aminopropyl)amino]quinazolin-2-yl}phenol, GLYCEROL, Serine/threonine-protein kinase pim-1 | | Authors: | Parker, L.J, Tanaka, A, Handa, N, Honda, K, Tomabechi, Y, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2013-07-10 | | Release date: | 2014-02-12 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.
Acta Crystallogr.,Sect.D, 70, 2014
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4ENY
 | | Crystal Structure of Pim-1 kinase in complex with (2E,5Z)-2-(2-chlorophenylimino)-5-(4-hydroxy-3-methoxybenzylidene)thiazolidin-4-one | | Descriptor: | (2Z,5Z)-2-[(2-chlorophenyl)imino]-5-(4-hydroxy-3-methoxybenzylidene)-1,3-thiazolidin-4-one, DIMETHYL SULFOXIDE, GLYCEROL, ... | | Authors: | Parker, L.J, Handa, N, Yokoyama, S. | | Deposit date: | 2012-04-13 | | Release date: | 2012-08-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.801 Å) | | Cite: | Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor
Acta Crystallogr.,Sect.F, 68, 2012
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3IXQ
 | | Structure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii | | Descriptor: | ACETATE ION, CHLORIDE ION, Ribose-5-phosphate isomerase A, ... | | Authors: | Antonyuk, S.V, Ellis, M.J, Strange, R.W, Hasnain, S.S, Bessho, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-09-04 | | Release date: | 2009-10-06 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.78 Å) | | Cite: | The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603).
Acta Crystallogr.,Sect.F, 65, 2009
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1AA9
 | | HUMAN C-HA-RAS(1-171)(DOT)GDP, NMR, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | C-HA-RAS, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION | | Authors: | Ito, Y, Yamasaki, Y, Muto, Y, Kawai, G, Nishimura, S, Miyazawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1997-01-27 | | Release date: | 1997-07-29 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
Biochemistry, 36, 1997
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2WQK
 | | Crystal Structure of Sure Protein from Aquifex aeolicus | | Descriptor: | 5'-NUCLEOTIDASE SURE, SODIUM ION, SULFATE ION | | Authors: | Antonyuk, S.V, Ellis, M.J, Strange, R.W, Hasnain, S.S, Bessho, Y, Kuramitsu, S, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-08-23 | | Release date: | 2009-09-29 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structure of Sure Protein from Aquifex Aeolicus Vf5 at 1.5 A Resolution.
Acta Crystallogr.,Sect.F, 65, 2009
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3JQJ
 | | Crystal structure of the molybdenum cofactor biosynthesis protein C (TTHA1789) from Thermus Theromophilus HB8 | | Descriptor: | GLYCEROL, Molybdenum cofactor biosynthesis protein C, PHOSPHATE ION, ... | | Authors: | Kanaujia, S.P, Jeyakanthan, J, Nakagawa, N, Sekar, K, Baba, S, Ebihara, A, Kuramitsu, S, Shinkai, A, Shiro, Y, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-09-07 | | Release date: | 2010-06-30 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8
Acta Crystallogr.,Sect.D, 66, 2010
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4ZU9
 | | Crystal structure of bacterial selenocysteine-specific elongation factor EF-Sec | | Descriptor: | CYSTEINE, Elongation factor SelB, MAGNESIUM ION, ... | | Authors: | Itoh, Y, Sekine, S, Yokoyama, S. | | Deposit date: | 2015-05-15 | | Release date: | 2015-09-23 | | Last modified: | 2020-02-19 | | Method: | X-RAY DIFFRACTION (3.191 Å) | | Cite: | Crystal structure of the full-length bacterial selenocysteine-specific elongation factor SelB
Nucleic Acids Res., 43, 2015
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3KB6
 | | Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid | | Descriptor: | D-lactate dehydrogenase, DI(HYDROXYETHYL)ETHER, GLYCEROL, ... | | Authors: | Antonyuk, S.V, Strange, R.W, Ellis, M.J, Bessho, Y, Kuramitsu, S, Yokoyama, S, Hasnain, S.S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2009-10-20 | | Release date: | 2009-11-10 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.12 Å) | | Cite: | Structure of D-lactate dehydrogenase from Aquifex aeolicus complexed with NAD(+) and lactic acid (or pyruvate).
Acta Crystallogr.,Sect.F, 65, 2009
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4LMU
 | | Crystal structure of Pim1 in complex with the inhibitor Quercetin (resulting from displacement of SKF86002) | | Descriptor: | 3,5,7,3',4'-PENTAHYDROXYFLAVONE, GLYCEROL, Serine/threonine-protein kinase pim-1 | | Authors: | Parker, L.J, Tanaka, A, Handa, N, Honda, K, Tomabechi, Y, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2013-07-11 | | Release date: | 2014-02-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.
Acta Crystallogr.,Sect.D, 70, 2014
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3VA2
 | | Crystal structure of human Interleukin-5 in complex with its alpha receptor | | Descriptor: | Interleukin-5, Interleukin-5 receptor subunit alpha | | Authors: | Kusano, S, Kukimoto-Niino, M, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2011-12-28 | | Release date: | 2012-07-25 | | Method: | X-RAY DIFFRACTION (2.703 Å) | | Cite: | Structural basis of interleukin-5 dimer recognition by its alpha receptor
Protein Sci., 21, 2012
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4LL5
 | | Crystal Structure of Pim-1 in complex with the fluorescent compound SKF86002 | | Descriptor: | 6-(4-fluorophenyl)-5-(pyridin-4-yl)-2,3-dihydroimidazo[2,1-b][1,3]thiazole, CALCIUM ION, GLYCEROL, ... | | Authors: | Parker, L.J, Tanaka, A, Handa, N, Honda, K, Tomabechi, Y, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2013-07-09 | | Release date: | 2014-02-12 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.
Acta Crystallogr.,Sect.D, 70, 2014
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4LUE
 | | Crystal Structure of HCK in complex with 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine (resulting from displacement of SKF86002) | | Descriptor: | 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Parker, L.J, Tanaka, A, Handa, N, Honda, K, Tomabechi, Y, Shirouzu, M, Yokoyama, S. | | Deposit date: | 2013-07-25 | | Release date: | 2014-02-12 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (3.04 Å) | | Cite: | Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.
Acta Crystallogr.,Sect.D, 70, 2014
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4ENX
 | | Crystal Structure of Pim-1 Kinase in complex with inhibitor (2E,5Z)-2-(2-chlorophenylimino)-5-(4-hydroxy-3-nitrobenzylidene)thiazolidin-4-one | | Descriptor: | (2Z,5Z)-2-[(2-chlorophenyl)imino]-5-(4-hydroxy-3-nitrobenzylidene)-1,3-thiazolidin-4-one, PHOSPHATE ION, Serine/threonine-protein kinase pim-1 | | Authors: | Parker, L.J, Handa, N, Yokoyama, S. | | Deposit date: | 2012-04-13 | | Release date: | 2012-08-08 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor
Acta Crystallogr.,Sect.F, 68, 2012
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2RV0
 | | Solution structures of the DNA-binding domain (ZF12) of immune-related zinc-finger protein ZFAT | | Descriptor: | ZINC ION, Zinc finger protein ZFAT | | Authors: | Tochio, N, Umehara, T, Kigawa, T, Yokoyama, S. | | Deposit date: | 2015-01-26 | | Release date: | 2015-04-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT
J.Struct.Funct.Genom., 16, 2015
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1N78
 | | Crystal structure of Thermus thermophilus glutamyl-tRNA synthetase complexed with tRNA(Glu) and glutamol-AMP. | | Descriptor: | GLUTAMOL-AMP, Glutamyl-tRNA synthetase, MAGNESIUM ION, ... | | 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: | 2002-11-13 | | Release date: | 2003-02-25 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.1 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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2RV6
 | | Solution structures of the DNA-binding domains (ZF2-ZF3-ZF4) of immune-related zinc-finger protein ZFAT | | Descriptor: | ZINC ION, Zinc finger protein ZFAT | | Authors: | Tochio, N, Umehara, T, Kigawa, T, Yokoyama, S. | | Deposit date: | 2015-01-26 | | Release date: | 2015-04-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT
J.Struct.Funct.Genom., 16, 2015
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2ROZ
 | | Structure of the C-terminal PID Domain of Fe65L1 Complexed with the Cytoplasmic Tail of APP Reveals a Novel Peptide Binding Mode | | Descriptor: | Amyloid beta A4 precursor protein-binding family B member 2, peptide from Amyloid beta A4 protein | | Authors: | Li, H, Koshiba, S, Tochio, N, Watanabe, S, Harada, T, Inoue, M, Kigawa, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2008-04-25 | | Release date: | 2008-07-22 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode
J.Biol.Chem., 283, 2008
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