Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
Search by PDB author
5D9B
DownloadVisualize
BU of 5d9b by Molmil
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against native data)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9D
DownloadVisualize
BU of 5d9d by Molmil
Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room temperature
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.701 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5D9C
DownloadVisualize
BU of 5d9c by Molmil
Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2015-08-18
Release date:2015-09-23
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.
Sci Rep, 5, 2015
5GTQ
DownloadVisualize
BU of 5gtq by Molmil
Luciferin-regenerating enzyme at cryogenic temperature
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, GLYCEROL, Luciferin regenerating enzyme, ...
Authors:Yamashita, K, Murai, T, Yamamoto, M, Gomi, K, Kajiyama, N, Kato, H, Nakatsu, T.
Deposit date:2016-08-23
Release date:2016-11-09
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.13 Å)
Cite:Luciferin-regenerating enzyme at cryogenic temperature
To Be Published
5XFE
DownloadVisualize
BU of 5xfe by Molmil
Luciferin-regenerating enzyme solved by SAD using XFEL (refined against 11,000 patterns)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Luciferin regenerating enzyme, MAGNESIUM ION, ...
Authors:Yamashita, K, Pan, D, Okuda, T, Murai, T, Kodan, A, Yamaguchi, T, Gomi, K, Kajiyama, N, Kato, H, Ago, H, Yamamoto, M, Nakatsu, T.
Deposit date:2017-04-10
Release date:2017-08-30
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography
IUCrJ, 4, 2017
3B07
DownloadVisualize
BU of 3b07 by Molmil
Crystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, Gamma-hemolysin component A, Gamma-hemolysin component B
Authors:Yamashita, K, Kawai, Y, Tanaka, Y, Yao, M, Tanaka, I.
Deposit date:2011-06-06
Release date:2011-10-12
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.495 Å)
Cite:Crystal structure of the octameric pore of staphylococcal gamma-hemolysin reveals the beta-barrel pore formation mechanism by two components
Proc.Natl.Acad.Sci.USA, 108, 2011
3A6J
DownloadVisualize
BU of 3a6j by Molmil
E122Q mutant creatininase complexed with creatine
Descriptor: Creatinine amidohydrolase, N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE, SULFATE ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6D
DownloadVisualize
BU of 3a6d by Molmil
Creatininase complexed with 1-methylguanidine
Descriptor: 1-METHYLGUANIDINE, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6F
DownloadVisualize
BU of 3a6f by Molmil
W174F mutant creatininase, Type II
Descriptor: CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6G
DownloadVisualize
BU of 3a6g by Molmil
W154F mutant creatininase
Descriptor: Creatinine amidohydrolase, MANGANESE (II) ION, ZINC ION
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6E
DownloadVisualize
BU of 3a6e by Molmil
W174F mutant creatininase, type I
Descriptor: CACODYLATE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6K
DownloadVisualize
BU of 3a6k by Molmil
The E122Q mutant creatininase, Mn-Zn type
Descriptor: CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6H
DownloadVisualize
BU of 3a6h by Molmil
W154A mutant creatininase
Descriptor: CHLORIDE ION, Creatinine amidohydrolase, MANGANESE (II) ION, ...
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-08-31
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
3A6L
DownloadVisualize
BU of 3a6l by Molmil
E122Q mutant creatininase, Zn-Zn type
Descriptor: CHLORIDE ION, Creatinine amidohydrolase, ZINC ION
Authors:Nakajima, Y, Yamashita, K, Ito, K, Yoshimoto, T.
Deposit date:2009-09-02
Release date:2010-02-09
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2 Å)
Cite:Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase
J.Mol.Biol., 396, 2010
7OWG
DownloadVisualize
BU of 7owg by Molmil
human DEPTOR in a complex with mutant human mTORC1 A1459P
Descriptor: DEP domain-containing mTOR-interacting protein, Regulatory-associated protein of mTOR, Serine/threonine-protein kinase mTOR, ...
Authors:Heimhalt, M, Berndt, A, Wagstaff, J, Anandapadamanaban, M, Perisic, O, Maslen, S, McLaughlin, S, Yu, W.-H, Masson, G.R, Boland, A, Ni, X, Yamashita, K, Murshudov, G.N, Skehel, M, Freund, S.M, Williams, R.L.
Deposit date:2021-06-18
Release date:2021-09-08
Last modified:2022-02-23
Method:ELECTRON MICROSCOPY (4.7 Å)
Cite:Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.
Elife, 10, 2021
6CSM
DownloadVisualize
BU of 6csm by Molmil
Crystal structure of the natural light-gated anion channel GtACR1
Descriptor: GtACR1, OLEIC ACID, RETINAL
Authors:Kato, H.E, Kim, Y, Yamashita, K, Kobilka, B.K, Deisseroth, K.
Deposit date:2018-03-21
Release date:2018-09-05
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural mechanisms of selectivity and gating in anion channelrhodopsins.
Nature, 561, 2018
6CSN
DownloadVisualize
BU of 6csn by Molmil
Crystal structure of the designed light-gated anion channel iC++ at pH8.5
Descriptor: CHLORIDE ION, OLEIC ACID, RETINAL, ...
Authors:Kato, H.E, Kim, Y, Yamashita, K, Kobilka, B.K, Deisseroth, K.
Deposit date:2018-03-21
Release date:2018-09-05
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Structural mechanisms of selectivity and gating in anion channelrhodopsins.
Nature, 561, 2018
6CSO
DownloadVisualize
BU of 6cso by Molmil
Crystal structure of the designed light-gated anion channel iC++ at pH6.5
Descriptor: OLEIC ACID, RETINAL, iC++
Authors:Kato, H.E, Kim, Y, Yamashita, K, Kobilka, B.K, Deisseroth, K.
Deposit date:2018-03-21
Release date:2018-09-05
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (3.2 Å)
Cite:Structural mechanisms of selectivity and gating in anion channelrhodopsins.
Nature, 561, 2018
6ZAV
DownloadVisualize
BU of 6zav by Molmil
NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 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 (1.19 Å)
Cite:An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
6ZAW
DownloadVisualize
BU of 6zaw by Molmil
Damage-free NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) determined by serial femtosecond rotation crystallography
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 (1.3 Å)
Cite:An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
6ZAR
DownloadVisualize
BU of 6zar by Molmil
As-isolated copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.1 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 (1.1 Å)
Cite:An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
6ZAX
DownloadVisualize
BU of 6zax by Molmil
Nitrite-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at low dose (0.5 MGy)
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 (1.48 Å)
Cite:An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures.
Sci Adv, 7, 2021
8W7N
DownloadVisualize
BU of 8w7n by Molmil
Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis
Descriptor: Pesticidal crystal protein Cry1Aa, UNKNOWN ATOM OR ION
Authors:Tanaka, J, Abe, S, Hayakawa, T, Kojima, M, Yamashita, K, Hirata, K, Ueno, T.
Deposit date:2023-08-31
Release date:2024-03-06
Method:X-RAY DIFFRACTION (3.6 Å)
Cite:Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis.
Biochem.Biophys.Res.Commun., 685, 2023
5ONY
DownloadVisualize
BU of 5ony by Molmil
As-isolated resting state copper nitrite reductase from Achromobacter xylosoxidans
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ...
Authors:Halsted, T.P, Yamashita, K, Hirata, K, Ago, H, Ueno, G, Tosha, T, Eady, R.R, Antonyuk, S.V, Yamamoto, M, Hasnain, S.S.
Deposit date:2017-08-04
Release date:2017-11-29
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.
IUCrJ, 5, 2018
5ONX
DownloadVisualize
BU of 5onx by Molmil
Resting state copper nitrite reductase determined by serial femtosecond rotation crystallography
Descriptor: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, COPPER (II) ION, Copper-containing nitrite reductase, ...
Authors:Halsted, T.P, Yamashita, K, Hirata, K, Ago, H, Ueno, G, Tosha, T, Eady, R.R, Antonyuk, S.V, Yamamoto, M, Hasnain, S.S.
Deposit date:2017-08-04
Release date:2017-11-29
Last modified:2024-01-17
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase.
IUCrJ, 5, 2018

217705

PDB entries from 2024-03-27

PDB statisticsPDBj update infoContact PDBjnumon