Loading
PDBj
English日本語简体中文繁體中文한국어
✖
ﾒﾆｭｰPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
PDB: 82 件
6Z1M
DownloadVisualize
BU of 6z1m by Molmil
Structure of an Ancestral glycosidase (family 1) bound to heme
分子名称: 1,2-ETHANEDIOL, Ancestral reconstructed glycosidase, GLYCEROL, ...
著者Gavira, J.A, Risso, V.A, Sanchez-Ruiz, J.M, Gamiz-Arco, G, Gutierrez-Rus, L, Ibarra-Molero, B, Oshino, Y, Petrovic, D, Romero-Rivera, A, Seelig, B, Kamerlin, S.C.L, Gaucher, E.A.
登録日2020-05-14
公開日2020-07-22
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (2.45 Å)
主引用文献Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Nat Commun, 12, 2021
5GKG
DownloadVisualize
BU of 5gkg by Molmil
Structure of EndoMS-dsDNA1'' complex
分子名称: (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*GP*GP*TP*CP*GP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*GP*TP*GP*TP*AP*GP*CP*G)-3'), ...
著者Nakae, S, Hijikata, A, Tsuji, T, Yonezawa, K, Kouyama, K, Mayanagi, K, Ishino, S, Ishino, Y, Shirai, T.
登録日2016-07-04
公開日2016-11-02
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Structure, 24, 2016
6Z1H
DownloadVisualize
BU of 6z1h by Molmil
Ancestral glycosidase (family 1)
分子名称: ANCESTRAL RECONSTRUCTED GLYCOSIDASE, GLYCEROL, ISOPROPYL ALCOHOL, ...
著者Gavira, J.A, Risso, V.A, Sanchez-Ruiz, J.M, Gamiz-Arco, G, Gutierrez-Rus, L, Ibarra-Molero, B, Hoshino, Y, Petrovic, D, Romero-Rivera, A, Seelig, B, Kamerlin, S.C.L, Gaucher, E.A.
登録日2020-05-13
公開日2020-07-22
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Nat Commun, 12, 2021
6JI2
DownloadVisualize
BU of 6ji2 by Molmil
Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex
分子名称: Archaeal ribosomal stalk protein aP1, Elongation factor 1-alpha, GUANOSINE-5'-TRIPHOSPHATE, ...
著者Maruyama, K, Imai, H, Kawamura, M, Ishino, S, Ishino, Y, Ito, K, Uchiumi, T.
登録日2019-02-20
公開日2019-11-13
最終更新日2023-11-22
実験手法X-RAY DIFFRACTION (3 Å)
主引用文献Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations.
Sci Rep, 9, 2019
6KNC
DownloadVisualize
BU of 6knc by Molmil
PolD-PCNA-DNA (form B)
分子名称: DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ...
著者Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y.
登録日2019-08-05
公開日2020-08-05
最終更新日2024-03-27
実験手法ELECTRON MICROSCOPY (9.3 Å)
主引用文献Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
6KNB
DownloadVisualize
BU of 6knb by Molmil
PolD-PCNA-DNA (form A)
分子名称: DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase II small subunit, DNA polymerase sliding clamp 1, ...
著者Mayanagi, K, Oki, K, Miyazaki, N, Ishino, S, Yamagami, T, Iwasaki, K, Kohda, D, Morikawa, K, Shirai, T, Ishino, Y.
登録日2019-08-05
公開日2020-08-05
最終更新日2021-02-17
実験手法ELECTRON MICROSCOPY (6.9 Å)
主引用文献Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18, 2020
1AN9
DownloadVisualize
BU of 1an9 by Molmil
D-AMINO ACID OXIDASE COMPLEX WITH O-AMINOBENZOATE
分子名称: 2-AMINOBENZOIC ACID, D-AMINO ACID OXIDASE, FLAVIN-ADENINE DINUCLEOTIDE
著者Miura, R, Setoyama, C, Nishina, Y, Shiga, K, Mizutani, H, Miyahara, I, Hirotsu, K.
登録日1997-06-28
公開日1997-11-12
最終更新日2023-11-15
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.
J.Biochem.(Tokyo), 122, 1997
1UDY
DownloadVisualize
BU of 1udy by Molmil
Medium-Chain Acyl-CoA Dehydrogenase with 3-Thiaoctanoyl-CoA
分子名称: 3-THIAOCTANOYL-COENZYME A, Acyl-CoA dehydrogenase, medium-chain specific, ...
著者Satoh, A, Nakajima, Y, Miyahara, I, Hirotsu, K, Tanaka, T, Nishina, Y, Shiga, K, Tamaoki, H, Setoyama, C, Miura, R.
登録日2003-05-07
公開日2003-12-09
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
J.BIOCHEM.(TOKYO), 134, 2003
1EVI
DownloadVisualize
BU of 1evi by Molmil
THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE
分子名称: 3,4-DIHYDRO-2H-PYRROLIUM-5-CARBOXYLATE, D-AMINO ACID OXIDASE, FLAVIN-ADENINE DINUCLEOTIDE
著者Mizutani, H, Miyahara, I, Hirotsu, K, Nishina, Y, Shiga, K, Setoyama, C, Miura, R.
登録日2000-04-20
公開日2000-10-23
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin.
J.Biochem.(Tokyo), 128, 2000
1DQ3
DownloadVisualize
BU of 1dq3 by Molmil
CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI
分子名称: ENDONUCLEASE, ZINC ION
著者Ichiyanagi, K, Ishino, Y, Morikawa, K.
登録日1999-12-30
公開日2000-07-05
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI.
J.Mol.Biol., 300, 2000
5CZC
DownloadVisualize
BU of 5czc by Molmil
The structure of VinK
分子名称: CALCIUM ION, GLYCEROL, Malonyl-CoA-[acyl-carrier-protein] transacylase
著者Miyanaga, A, Iwasawa, S, Shinohara, Y, Kudo, F, Eguchi, T.
登録日2015-07-31
公開日2016-02-03
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.
Proc.Natl.Acad.Sci.USA, 113, 2016
5CZD
DownloadVisualize
BU of 5czd by Molmil
The complex structure of VinK with VinL
分子名称: 1,1'-ethane-1,2-diyldipyrrolidine-2,5-dione, 4'-PHOSPHOPANTETHEINE, Acyl-carrier-protein, ...
著者Miyanaga, A, Iwasawa, S, Shinohara, Y, Kudo, F, Eguchi, T.
登録日2015-07-31
公開日2016-02-03
最終更新日2023-11-08
実験手法X-RAY DIFFRACTION (2.34 Å)
主引用文献Structure-based analysis of the molecular interactions between acyltransferase and acyl carrier protein in vicenistatin biosynthesis.
Proc.Natl.Acad.Sci.USA, 113, 2016
1GE8
DownloadVisualize
BU of 1ge8 by Molmil
PROLIFERATING CELL NUCLEAR ANTIGEN (PCNA) HOMOLOG FROM PYROCOCCUS FURIOSUS
分子名称: PROLIFERATION CELL NUCLEAR ANTIGEN
著者Matsumiya, S, Ishino, Y, Morikawa, K.
登録日2000-10-18
公開日2001-01-24
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus.
Protein Sci., 10, 2001
6Y1L
DownloadVisualize
BU of 6y1l by Molmil
Crystal structure of the paraoxon-modified A.17 antibody FAB fragment - L47R mutant
分子名称: DIETHYL PHOSPHONATE, FAB A.17 L47R mutant HEAVY CHAIN, FAB A.17 L47R mutant Light CHAIN, ...
著者Chatziefthimiou, S, Mokrushina, Y, Smirnov, I, Gabibov, A, Wilmanns, M.
登録日2020-02-12
公開日2020-09-23
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (1.4 Å)
主引用文献Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Proc.Natl.Acad.Sci.USA, 117, 2020
6Y49
DownloadVisualize
BU of 6y49 by Molmil
Crystal structure of the paraoxon-modified A.17kappa antibody FAB fragment
分子名称: A.17kappa antibody FAB fragment - Heavy Chain, A.17kappa antibody FAB fragment - Light Chain, DIETHYL PHOSPHONATE
著者Chatziefthimiou, S, Mokrushina, Y, Smirnov, I, Gabibov, A, Wilmanns, M.
登録日2020-02-19
公開日2020-09-16
最終更新日2020-09-30
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Proc.Natl.Acad.Sci.USA, 117, 2020
6Y1K
DownloadVisualize
BU of 6y1k by Molmil
Crystal structure of the unmodified A.17 antibody FAB fragment - L47R mutant
分子名称: FAB A.17 L47R mutant Heavy Chain, FAB A.17 L47R mutant Light Chain
著者Chatziefthimiou, S, Stepanova, A, Mokrushina, Y, Smirnov, I, Gabibov, A, Wilmanns, M.
登録日2020-02-12
公開日2020-09-16
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Proc.Natl.Acad.Sci.USA, 117, 2020
6Y1M
DownloadVisualize
BU of 6y1m by Molmil
Crystal structure of the paraoxon-modified A.17 antibody FAB fragment - L47K mutant
分子名称: DIETHYL PHOSPHONATE, FAB A.17 L47K mutant HEAVY CHAIN, FAB A.17 L47K mutant Light CHAIN
著者Chatziefthimiou, S, Mokrushina, Y, Smirnov, I, Gabibov, A, Wilmanns, M.
登録日2020-02-12
公開日2020-09-16
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Proc.Natl.Acad.Sci.USA, 117, 2020
6Y1N
DownloadVisualize
BU of 6y1n by Molmil
Crystal structure of the phosphonate-modified A.5 antibody FAB fragment
分子名称: 8-METHYL-8-AZABICYCLO[3.2.1]OCTAN-3-YL PHENYLPHOSPHONATE, FAB A.5 Heavy chain, FAB A.5 Light Chain
著者Chatziefthimiou, S, Mokrushina, Y, Smirnov, I, Gabibov, A, Wilmanns, M.
登録日2020-02-12
公開日2020-09-23
最終更新日2024-01-24
実験手法X-RAY DIFFRACTION (2.2 Å)
主引用文献Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Proc.Natl.Acad.Sci.USA, 117, 2020
2CFM
DownloadVisualize
BU of 2cfm by Molmil
ATP-DEPENDENT DNA LIGASE FROM PYROCOCCUS FURIOSUS
分子名称: ADENOSINE MONOPHOSPHATE, MAGNESIUM ION, THERMOSTABLE DNA LIGASE
著者Nishida, H, Ishino, Y, Morikawa, K.
登録日2006-02-22
公開日2006-07-12
最終更新日2019-02-06
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献The Closed Structure of an Archaeal DNA Ligase from Pyrococcus Furiosus.
J.Mol.Biol., 360, 2006
1VE9
DownloadVisualize
BU of 1ve9 by Molmil
Porcine kidney D-amino acid oxidase
分子名称: BENZOIC ACID, D-amino acid oxidase, FLAVIN-ADENINE DINUCLEOTIDE
著者Mizutani, H, Miyahara, I, Hirotsu, K, Nishina, Y, Shiga, K, Setoyama, C, Miura, R.
登録日2004-03-29
公開日2004-04-13
最終更新日2023-12-27
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution.
J.Biochem., 120, 1996
3A2F
DownloadVisualize
BU of 3a2f by Molmil
Crystal Structure of Pyrococcus furiosus DNA polymerase/PCNA monomer mutant complex
分子名称: DNA polymerase, DNA polymerase sliding clamp
著者Nishida, H, Ishino, Y, Morikawa, K.
登録日2009-05-15
公開日2009-11-03
最終更新日2021-11-10
実験手法X-RAY DIFFRACTION (2.67 Å)
主引用文献Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex
To be Published
7E15
DownloadVisualize
BU of 7e15 by Molmil
Protein ternary complex working for DNA replication initiation
分子名称: DNA polymerase II small subunit, Gins51, SsDNA-specific exonuclease
著者Oyama, T, Ishino, Y.
登録日2021-01-30
公開日2021-10-06
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (2.45 Å)
主引用文献Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome.
Nucleic Acids Res., 50, 2022
7DD4
DownloadVisualize
BU of 7dd4 by Molmil
Solution structure of an RNA derived from the joint region of the TAR and PolyA stems of HIV-1 genomic RNA
分子名称: RNA (36-MER)
著者Obayashi, C.M, Shinohara, Y, Masuda, T, Kawai, G.
登録日2020-10-27
公開日2021-06-09
最終更新日2024-05-15
実験手法SOLUTION NMR
主引用文献Influence of the 5'-terminal sequences on the 5'-UTR structure of HIV-1 genomic RNA.
Sci Rep, 11, 2021
2ZJ2
DownloadVisualize
BU of 2zj2 by Molmil
Archaeal DNA helicase Hjm apo state in form 1
分子名称: Putative ski2-type helicase, SULFATE ION
著者Oyama, T, Oka, H, Fujikane, R, Ishino, Y, Morikawa, K.
登録日2008-02-29
公開日2009-02-10
最終更新日2024-03-13
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm
Bmc Struct.Biol., 9, 2009
2ZJ8
DownloadVisualize
BU of 2zj8 by Molmil
Archaeal DNA helicase Hjm apo state in form 2
分子名称: Putative ski2-type helicase
著者Oyama, T, Oka, H, Fujikane, R, Ishino, Y, Morikawa, K.
登録日2008-02-29
公開日2009-02-10
最終更新日2023-11-01
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm
Bmc Struct.Biol., 9, 2009

226707

件を2024-10-30に公開中

PDB statisticsPDBj update infoContact PDBjnumon