6ZAU
 
 | | Damage-free nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, GLYCEROL, ... | | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2020-06-05 | | Release date: | 2021-01-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
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6ZAS
 | | Damage-free as-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography | | Descriptor: | COPPER (II) ION, Copper-containing nitrite reductase, SULFATE ION | | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2020-06-05 | | Release date: | 2021-01-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.3 Å) | | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
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6ZAT
 | | Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.0 A resolution (unrestrained full matrix refinement by SHELX) | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ... | | Authors: | Rose, S.L, Antonyuk, S.V, Sasaki, D, Yamashita, K, Hirata, K, Ueno, G, Ago, H, Eady, R.R, Tosha, T, Yamamoto, M, Hasnain, S.S. | | Deposit date: | 2020-06-05 | | Release date: | 2021-01-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1 Å) | | Cite: | An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
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8J81
 | | MDM2 bound with a peptoid | | Descriptor: | (2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(phenylmethyl)amino]propanoyl]-methyl-amino]propanoyl]amino]propanoyl]-methyl-amino]-N-(3,3-dimethylbutyl)-N-[(2S)-1-oxidanylidene-1-piperazin-1-yl-propan-2-yl]propanamide, CHLORIDE ION, E3 ubiquitin-protein ligase Mdm2 | | Authors: | Yokomine, M, Fukuda, Y, Ago, H, Matsuura, H, Ueno, G, Nagatoishi, S, Yamamoto, M, Tsumoto, K, Jumpei, M, Sando, S. | | Deposit date: | 2023-04-28 | | Release date: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | A structural and physicochemical study of how a peptoid binds to a protein
To Be Published
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1K1V
 | | Solution Structure of the DNA-Binding Domain of MafG | | Descriptor: | MafG | | Authors: | Kusunoki, H, Motohashi, H, Katsuoka, F, Morohashi, A, Yamamoto, M, Tanaka, T. | | Deposit date: | 2001-09-25 | | Release date: | 2002-04-10 | | Last modified: | 2022-02-23 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the DNA-binding domain of MafG.
Nat.Struct.Biol., 9, 2002
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1K1X
 | | Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 4-ALPHA-GLUCANOTRANSFERASE, CALCIUM ION | | Authors: | Imamura, H, Fushinobu, S, Kumasaka, T, Yamamoto, M, Jeon, B.S, Wakagi, T, Matsuzawa, H. | | Deposit date: | 2001-09-26 | | Release date: | 2003-06-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor
J.BIOL.CHEM., 278, 2003
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1K1W
 | | Crystal structure of 4-alpha-glucanotransferase from thermococcus litoralis | | Descriptor: | 4-ALPHA-GLUCANOTRANSFERASE, CALCIUM ION, SULFATE ION, ... | | Authors: | Imamura, H, Fushinobu, S, Kumasaka, T, Yamamoto, M, Jeon, B.S, Wakagi, T, Matsuzawa, H. | | Deposit date: | 2001-09-26 | | Release date: | 2003-06-17 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor
J.BIOL.CHEM., 278, 2003
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1K1Y
 | | Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, 4-ALPHA-GLUCANOTRANSFERASE, ... | | Authors: | Imamura, H, Fushinobu, S, Kumasaka, T, Yamamoto, M, Jeon, B.S, Wakagi, T, Matsuzawa, H. | | Deposit date: | 2001-09-26 | | Release date: | 2003-06-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor
J.BIOL.CHEM., 278, 2003
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6I59
 | | Long wavelength native-SAD phasing of Sen1 helicase | | Descriptor: | 1,2-ETHANEDIOL, ADENOSINE-5'-DIPHOSPHATE, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Basu, S, Olieric, V, Matsugaki, N, Kawano, Y, Takashi, T, Huang, C.Y, Leonarski, F, Yamada, Y, Vera, L, Olieric, N, Basquin, J, Wojdyla, J.A, Diederichs, K, Yamamoto, M, Bunk, O, Wang, M. | | Deposit date: | 2018-11-13 | | Release date: | 2019-03-13 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6, 2019
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6QQ5
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans | | Descriptor: | CALCIUM ION, FE (III) ION, Nitric oxide reductase subunit B, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.9 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
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6QQ6
 | | Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) Val495Ala mutant from Alcaligenes xylosoxidans | | Descriptor: | (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE, CALCIUM ION, DODECYL-BETA-D-MALTOSIDE, ... | | Authors: | Gopalasingam, C.C, Johnson, R.M, Chiduza, G.N, Tosha, T, Yamamoto, M, Shiro, Y, Antonyuk, S.V, Muench, S.P, Hasnain, S.S. | | Deposit date: | 2019-02-17 | | Release date: | 2019-09-11 | | Last modified: | 2024-05-15 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy.
Sci Adv, 5, 2019
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1WNI
 | | Crystal Structure of H2-Proteinase | | Descriptor: | Trimerelysin II, ZINC ION | | Authors: | Kumasaka, T, Yamamoto, M, Moriyama, H, Tanaka, N, Sato, M, Katsube, Y, Yamakawa, Y, Omori-Satoh, T, Iwanaga, S, Ueki, T. | | Deposit date: | 2004-08-04 | | Release date: | 2004-08-17 | | Last modified: | 2019-10-09 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.
J.Biochem., 119, 1996
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6I5C
 | | Long wavelength native-SAD phasing of Tubulin-Stathmin-TTL complex | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CALCIUM ION, CHLORIDE ION, ... | | Authors: | Basu, S, Olieric, V, Matsugaki, N, Kawano, Y, Takashi, T, Huang, C.Y, Leonarski, F, Yamada, Y, Vera, L, Olieric, N, Basquin, J, Wojdyla, J.A, Diederichs, K, Yamamoto, M, Bunk, O, Wang, M. | | Deposit date: | 2018-11-13 | | Release date: | 2019-03-13 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | Long-wavelength native-SAD phasing: opportunities and challenges.
Iucrj, 6, 2019
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1V3V
 | | Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complexed with NADP and 15-oxo-PGE2 | | Descriptor: | (5E,13E)-11-HYDROXY-9,15-DIOXOPROSTA-5,13-DIEN-1-OIC ACID, CHLORIDE ION, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... | | Authors: | Hori, T, Yokomizo, T, Ago, H, Sugahara, M, Ueno, G, Yamamoto, M, Kumasaka, T, Shimizu, T, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-11-06 | | Release date: | 2004-07-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
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1V3T
 | | Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase | | Descriptor: | NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase | | Authors: | Hori, T, Yokomizo, T, Ago, H, Sugahara, M, Ueno, G, Yamamoto, M, Kumasaka, T, Shimizu, T, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-11-05 | | Release date: | 2004-07-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
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1V26
 | | Crystal structure of tt0168 from Thermus thermophilus HB8 | | Descriptor: | ADENOSINE MONOPHOSPHATE, MAGNESIUM ION, MYRISTIC ACID, ... | | Authors: | Hisanaga, Y, Ago, H, Nakatsu, T, Hamada, K, Ida, K, Kanda, H, Yamamoto, M, Hori, T, Arii, Y, Sugahara, M, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-07 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structural Basis of the Substrate-specific Two-step Catalysis of Long Chain Fatty Acyl-CoA Synthetase Dimer
J.Biol.Chem., 279, 2004
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1ULU
 | | Crystal structure of tt0143 from Thermus thermophilus HB8 | | Descriptor: | enoyl-acyl carrier protein reductase | | Authors: | Ago, H, Hamada, K, Ida, K, Kanda, H, Sugahara, M, Yamamoto, M, Nodake, Y, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-16 | | Release date: | 2004-11-02 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of tt0143 from Thermus thermophilus HB8
To be Published
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1ULT
 | | Crystal structure of tt0168 from Thermus thermophilus HB8 | | Descriptor: | CITRIC ACID, long chain fatty acid-CoA ligase | | Authors: | Hisanaga, Y, Ago, H, Nakatsu, T, Hamada, K, Ida, K, Kanda, H, Yamamoto, M, Hori, T, Arii, Y, Sugahara, M, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-16 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.55 Å) | | Cite: | Structural basis of the substrate specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer
J.Biol.Chem., 279, 2004
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1ULQ
 | | Crystal structure of tt0182 from Thermus thermophilus HB8 | | Descriptor: | putative acetyl-CoA acetyltransferase | | Authors: | Ago, H, Hamada, K, Ida, K, Kanda, H, Sugahara, M, Yamamoto, M, Kuroishi, C, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-09-16 | | Release date: | 2004-11-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Crystal structure of tt0182 from Thermus thermophilus HB8
To be Published
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1V25
 | | Crystal structure of tt0168 from Thermus thermophilus HB8 | | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, long-chain-fatty-acid-CoA synthetase | | Authors: | Hisanaga, Y, Ago, H, Nakatsu, T, Hamada, K, Ida, K, Kanda, H, Yamamoto, M, Hori, T, Arii, Y, Sugahara, M, Kuramitsu, S, Yokoyama, S, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-10-07 | | Release date: | 2004-07-27 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural Basis of the Substrate-specific Two-step Catalysis of Long Chain Fatty Acyl-CoA Synthetase Dimer
J.Biol.Chem., 279, 2004
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1V3U
 | | Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase in apo form | | Descriptor: | CHLORIDE ION, leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase | | Authors: | Hori, T, Yokomizo, T, Ago, H, Sugahara, M, Ueno, G, Yamamoto, M, Kumasaka, T, Shimizu, T, Miyano, M, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2003-11-05 | | Release date: | 2004-07-13 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
J.Biol.Chem., 279, 2004
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1WN5
 | | Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Cacodylic Acid | | Descriptor: | Blasticidin-S deaminase, CACODYLATE ION, ZINC ION | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2004-07-27 | | Release date: | 2005-10-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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1WN6
 | | Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S | | Descriptor: | 6-(4-AMINO-4-HYDROXY-2-OXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-3-[3-AMINO-5-(N-METHYL-GUANIDINO)-PENT ANOYLAMINO]-3,6-DIHYDRO-2H-PYRAN-2-CARBOXYLIC ACID, ARSENIC, Blasticidin-S deaminase, ... | | Authors: | Kumasaka, T, Yamamoto, M, Furuichi, M, Nakasako, M, Kimura, M, Yamaguchi, I, Ueki, T. | | Deposit date: | 2004-07-27 | | Release date: | 2005-10-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc
J.Biol.Chem., 282, 2007
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6LPK
 | | A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a, CHOLESTEROL, ... | | Authors: | Ihara, K, Hato, M, Nakane, T, Yamashita, K, Kimura-Someya, T, Hosaka, T, Ishizuka-Katsura, Y, Tanaka, R, Tanaka, T, Sugahara, M, Hirata, K, Yamamoto, M, Nureki, O, Tono, K, Nango, E, Iwata, S, Shirouzu, M. | | Deposit date: | 2020-01-10 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Sci Rep, 10, 2020
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6LPJ
 | | A2AR crystallized in EROCOC17+4, LCP-SFX at 277 K | | Descriptor: | 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol, Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a, CHOLESTEROL, ... | | Authors: | Ihara, K, Hato, M, Nakane, T, Yamashita, K, Kimura-Someya, T, Hosaka, T, Ishizuka-Katsura, Y, Tanaka, R, Tanaka, T, Sugahara, M, Hirata, K, Yamamoto, M, Nureki, O, Tono, K, Nango, E, Iwata, S, Shirouzu, M. | | Deposit date: | 2020-01-10 | | Release date: | 2020-11-25 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Sci Rep, 10, 2020
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