2PCK
 
 | | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, diphthine synthase | | Authors: | Yamamoto, H, Morikawa, Y, Matsuura, Y, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-30 | | Release date: | 2007-10-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3
To be Published
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5AXO
 | | Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem | | Descriptor: | (2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-(dimethylcarbamoy l)pyrrolidin-3-yl]sulfanyl-3-methyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Metallo-beta-lactamase, ... | | Authors: | Wachino, J, Arakawa, Y. | | Deposit date: | 2015-07-31 | | Release date: | 2016-05-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.39 Å) | | Cite: | Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Meropenem
To Be Published
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5B1U
 | | Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Imipenem | | Descriptor: | (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid, Metallo-beta-lactamase, SODIUM ION, ... | | Authors: | Wachino, J, Arakawa, Y. | | Deposit date: | 2015-12-20 | | Release date: | 2016-05-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Crystal Structure of Metallo-beta-Lactamase SMB-1 Bound to Hydrolyzed Imipenem
To be published
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5AYH
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2KFJ
 | | Solution structure of the loop deletion mutant of PB1 domain of Cdc24p | | Descriptor: | Cell division control protein 24 | | Authors: | Ogura, K, Tandai, T, Yoshinaga, S, Kobashigawa, Y, Kumeta, H, Inagaki, F. | | Deposit date: | 2009-02-22 | | Release date: | 2009-10-06 | | Last modified: | 2024-05-29 | | Method: | SOLUTION NMR | | Cite: | NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae
J.Biochem., 146, 2009
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1V9T
 | | Structure of E. coli cyclophilin B K163T mutant bound to succinyl-ALA-PRO-ALA-P-nitroanilide | | Descriptor: | (SIN)APA(NIT), cyclophilin B | | Authors: | Konno, M, Sano, Y, Okudaira, K, Kawaguchi, Y, Yamagishi-Ohmori, Y, Fushinobu, S, Matsuzawa, H. | | Deposit date: | 2004-02-03 | | Release date: | 2004-09-21 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer
Eur.J.Biochem., 271, 2004
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1VAI
 | | Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin | | Descriptor: | (ACE)AAPA(MCM), cyclophilin B | | Authors: | Konno, M, Sano, Y, Okudaira, K, Kawaguchi, Y, Yamagishi-Ohmori, Y, Fushinobu, S, Matsuzawa, H. | | Deposit date: | 2004-02-17 | | Release date: | 2004-09-21 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer
Eur.J.Biochem., 271, 2004
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6L4P
 | | Crystal structure of the complex between the axonemal outer-arm dynein light chain-1 and microtubule binding domain of gamma heavy chain | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Dynein light chain 1, axonemal, ... | | Authors: | Toda, A, Nishikawa, Y, Tanaka, H, Yagi, T, Kurisu, G. | | Deposit date: | 2019-10-19 | | Release date: | 2020-02-19 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.703 Å) | | Cite: | The complex of outer-arm dynein light chain-1 and the microtubule-binding domain of the gamma heavy chain shows how axonemal dynein tunes ciliary beating.
J.Biol.Chem., 295, 2020
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6L2F
 | | Crystal structure of a cupin protein (tm1459, H54AH58A mutant) in copper (Cu) substituted form | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL, COPPER (II) ION, ... | | Authors: | Fujieda, N, Ichihashi, H, Nishikawa, Y, Kurisu, G, Itoh, S. | | Deposit date: | 2019-10-03 | | Release date: | 2020-04-01 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.23 Å) | | Cite: | Cupin Variants as a Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes.
Angew.Chem.Int.Ed.Engl., 59, 2020
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2LDR
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3VGT
 | | Wild-type nucleoside diphosphate kinase derived from Halomonas sp. 593 | | Descriptor: | Nucleoside diphosphate kinase | | Authors: | Okazaki, N, Yonezawa, Y, Arai, S, Matsumoto, F, Tamada, T, Tokunaga, H, Ishibashi, M, Tokunaga, M, Kuroki, R. | | Deposit date: | 2011-08-21 | | Release date: | 2012-07-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase
Protein Sci., 21, 2012
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3WO5
 | | Crystal structure of S147Q of Rv2613c from Mycobacterium tuberculosis | | Descriptor: | AP-4-A phosphorylase, GLYCEROL, PHOSPHATE ION, ... | | Authors: | Mori, S, Wachino, J, Arakawa, Y, Shibayama, K. | | Deposit date: | 2013-12-20 | | Release date: | 2014-12-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.79 Å) | | Cite: | Role of Ser-147 and Ala-149 in catalytic activity of diadenosine tetraphosphate phosphorylase from Mycobacterium tuberculosis H37Rv
To be Published
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8GBJ
 | | Cryo-EM structure of a human BCDX2/ssDNA complex | | Descriptor: | DNA (5'-D(P*CP*CP*CP*CP*CP*C)-3'), DNA repair protein RAD51 homolog 2, DNA repair protein RAD51 homolog 3, ... | | Authors: | Jia, L, Wasmuth, E.V, Ruben, E.A, Sung, P, Rawal, Y, Greene, E.C, Meir, A, Olsen, S.K. | | Deposit date: | 2023-02-26 | | Release date: | 2023-06-21 | | Last modified: | 2023-08-02 | | Method: | ELECTRON MICROSCOPY (3.11 Å) | | Cite: | Structural insights into BCDX2 complex function in homologous recombination.
Nature, 619, 2023
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7WWT
 | | Cu/Zn-superoxide dismutase from dog (Canis familiaris) | | Descriptor: | COPPER (II) ION, Superoxide dismutase [Cu-Zn], ZINC ION | | Authors: | Narikiyo, S, Furukawa, Y, Akutsu, M. | | Deposit date: | 2022-02-14 | | Release date: | 2023-02-15 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Intrinsic structural vulnerability in the hydrophobic core induces species-specific aggregation of canine SOD1 with degenerative myelopathy-linked E40K mutation.
J.Biol.Chem., 299, 2023
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7WWY
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7WX0
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7WX1
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8FAZ
 | | Cryo-EM structure of the human BCDX2 complex | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DNA repair protein RAD51 homolog 2, DNA repair protein RAD51 homolog 3, ... | | Authors: | Jia, L, Wasmuth, E.V, Ruben, E.A, Sung, P, Rawal, Y, Greene, E.C, Meir, A, Olsen, S.K. | | Deposit date: | 2022-11-29 | | Release date: | 2023-06-21 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (2.3 Å) | | Cite: | Structural insights into BCDX2 complex function in homologous recombination.
Nature, 619, 2023
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2P6I
 | | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | S-ADENOSYL-L-HOMOCYSTEINE, diphthine synthase | | Authors: | Yamamoto, H, Matsuura, Y, Morikawa, Y, Shimada, H, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-18 | | Release date: | 2007-09-18 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3
To be Published
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1DIZ
 | | CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) COMPLEXED WITH DNA | | Descriptor: | 3-METHYLADENINE DNA GLYCOSYLASE II, DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3'), DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3'), ... | | Authors: | Hollis, T, Ichikawa, Y, Ellenberger, T.E. | | Deposit date: | 1999-11-30 | | Release date: | 2000-03-20 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
EMBO J., 19, 2000
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2PCI
 | | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | | Descriptor: | Probable diphthine synthase, S-ADENOSYL-L-HOMOCYSTEINE | | Authors: | Yamamoto, H, Matsuura, Y, Morikawa, Y, Nakamoto, T, Kunishima, N, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2007-03-29 | | Release date: | 2007-10-02 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystal structure of PH0725 from Pyrococcus horikoshii OT3
To be Published
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3VGU
 | | E134A mutant nucleoside diphosphate kinase derived from Halomonas sp. 593 | | Descriptor: | Nucleoside diphosphate kinase | | Authors: | Okazaki, N, Yonezawa, Y, Arai, S, Matsumoto, F, Tamada, T, Tokunaga, H, Ishibashi, M, Tokunaga, M, Kuroki, R. | | Deposit date: | 2011-08-21 | | Release date: | 2012-07-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase
Protein Sci., 21, 2012
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5X33
 | | Leukotriene B4 receptor BLT1 in complex with BIIL260 | | Descriptor: | 4-[[3-[[4-[2-(4-hydroxyphenyl)propan-2-yl]phenoxy]methyl]phenyl]methoxy]benzenecarboximidamide, LTB4 receptor,Lysozyme,LTB4 receptor | | Authors: | Hori, T, Hirata, K, Yamashita, K, Kawano, Y, Yamamoto, M, Yokoyama, S. | | Deposit date: | 2017-02-03 | | Release date: | 2018-01-03 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | Na+-mimicking ligands stabilize the inactive state of leukotriene B4receptor BLT1.
Nat. Chem. Biol., 14, 2018
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8H0W
 | | RNA polymerase II transcribing a chromatosome (type II) | | Descriptor: | DNA (261-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Hirano, R, Ehara, H, Tomoya, K, Takizawa, Y, Sekine, S, Kurumizaka, H. | | Deposit date: | 2022-09-30 | | Release date: | 2022-12-07 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (4.6 Å) | | Cite: | Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1.
Nat Commun, 13, 2022
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8H0V
 | | RNA polymerase II transcribing a chromatosome (type I) | | Descriptor: | DNA (261-MER), DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase subunit beta, ... | | Authors: | Hirano, R, Ehara, H, Tomoya, K, Takizawa, Y, Sekine, S, Kurumizaka, H. | | Deposit date: | 2022-09-30 | | Release date: | 2022-12-07 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1.
Nat Commun, 13, 2022
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