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PDB: 210 results
7SI9
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BU of 7si9 by Molmil
Room temperature X-ray structure of SARS-CoV-2 main protease (Mpro) in complex with PF-07321332
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase
Authors:Kovalevsky, A, Kneller, D.W, Coates, L.
Deposit date:2021-10-12
Release date:2021-10-20
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease
Nat Commun, 13, 2022
3KMF
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BU of 3kmf by Molmil
Room Temperature Time-of-Flight Neutron Diffraction Study of Deoxy Human Normal Adult Hemoglobin
Descriptor: Hemoglobin subunit alpha, Hemoglobin subunit beta, PROTOPORPHYRIN IX CONTAINING FE
Authors:Kovalevsky, A.Y, Morimoto, Y, Chatake, T.
Deposit date:2009-11-10
Release date:2010-04-21
Last modified:2023-11-01
Method:NEUTRON DIFFRACTION (2 Å)
Cite:Direct Determination of Protonation States of Histidine Residues in a 2 A Neutron Structure of Deoxy-Human Normal Adult Hemoglobin and Implications for the Bohr Effect.
J.Mol.Biol., 398, 2010
7S4B
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BU of 7s4b by Molmil
Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724963
Descriptor: (2R)-2-(3-fluorophenyl)-N-(isoquinolin-4-yl)propanamide, 3C-like proteinase
Authors:Kovalevsky, A, Kneller, D.W, Coates, L.
Deposit date:2021-09-08
Release date:2021-09-15
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.
Acs Pharmacol Transl Sci, 5, 2022
7S3S
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BU of 7s3s by Molmil
Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530724813
Descriptor: 2-(3-chlorophenyl)-N-(isoquinolin-4-yl)acetamide, 3C-like proteinase
Authors:Kovalevsky, A, Kneller, D.W, Coates, L.
Deposit date:2021-09-08
Release date:2021-09-15
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2 Å)
Cite:Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.
Acs Pharmacol Transl Sci, 5, 2022
7S3K
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BU of 7s3k by Molmil
Room temperature X-ray structure of SARS-CoV-2 main protease in complex with compound Z1530718726
Descriptor: 2-(5-chloro-2-methoxyphenyl)-N-(isoquinolin-4-yl)acetamide, 3C-like proteinase
Authors:Kovalevsky, A, Kneller, D.W, Coates, L.
Deposit date:2021-09-07
Release date:2021-09-15
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor.
Acs Pharmacol Transl Sci, 5, 2022
7JUN
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BU of 7jun by Molmil
Joint neutron/X-ray structure of SARS-CoV-2 3CL Mpro at room temperature
Descriptor: 3C-like proteinase
Authors:Kovalevsky, A, Kneller, D.W, Coates, L.
Deposit date:2020-08-20
Release date:2020-09-02
Last modified:2024-04-03
Method:NEUTRON DIFFRACTION (2.3 Å), X-RAY DIFFRACTION
Cite:Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography.
J.Biol.Chem., 295, 2020
3KBS
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BU of 3kbs by Molmil
Room Temperature X-ray structure of D-Xylose Isomerase in complex with 2Cd(2+) co-factors
Descriptor: CADMIUM ION, Xylose isomerase
Authors:Kovalevsky, A.Y, Hanson, L, Langan, P.
Deposit date:2009-10-20
Release date:2010-06-16
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KBV
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BU of 3kbv by Molmil
Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors
Descriptor: NICKEL (II) ION, Xylose isomerase
Authors:Kovalevsky, A.Y, Hanson, L, Langan, P.
Deposit date:2009-10-20
Release date:2010-06-16
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KBW
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BU of 3kbw by Molmil
Room temperature X-ray mixed-metal structure of D-Xylose Isomerase in complex with Ni(2+) and Mg(2+) co-factors
Descriptor: MAGNESIUM ION, NICKEL (II) ION, Xylose isomerase
Authors:Kovalevsky, A.Y, Hanson, L, Langan, P.
Deposit date:2009-10-20
Release date:2010-06-16
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KBM
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BU of 3kbm by Molmil
Room Temperature X-ray structure of D-Xylose Isomerase complexed with 2Cd(2+) co-factors and d12-D-alpha-glucose in the cyclic form
Descriptor: CADMIUM ION, Xylose isomerase, alpha-D-glucopyranose
Authors:Kovalevsky, A.Y, Hanson, L, Langan, P.
Deposit date:2009-10-20
Release date:2010-06-16
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2 Å)
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KCL
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BU of 3kcl by Molmil
Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)
Descriptor: CADMIUM ION, Xylose isomerase, alpha-D-glucopyranose
Authors:Kovalevsky, A.Y, Langan, P.
Deposit date:2009-10-21
Release date:2010-06-16
Last modified:2024-04-03
Method:NEUTRON DIFFRACTION (2 Å), X-RAY DIFFRACTION
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KCO
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BU of 3kco by Molmil
Room temperature neutron structure of D-Xylose Isomerase in complex with two Ni2+ cations and d12-D-glucose in the linear form (refined jointly with X-ray structure 3KBN)
Descriptor: D-glucose, NICKEL (II) ION, Xylose isomerase
Authors:Kovalevsky, A.Y, Langan, P.
Deposit date:2009-10-21
Release date:2010-06-16
Last modified:2024-04-03
Method:NEUTRON DIFFRACTION (1.8 Å), X-RAY DIFFRACTION
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KBN
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BU of 3kbn by Molmil
Room temperature structure of D-Xylose Isomerase in complex with 2Ni(2+) co-factors and d12-D-glucose in the linear form
Descriptor: D-glucose, NICKEL (II) ION, Xylose isomerase
Authors:Kovalevsky, A.Y, Hanson, L, Langan, P.
Deposit date:2009-10-20
Release date:2010-06-16
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (1.53 Å)
Cite:Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
Structure, 18, 2010
3KCJ
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BU of 3kcj by Molmil
Room temperature neutron structure of apo-D-Xylose Isomerase (refined jointly with X-ray structure 3KBJ)
Descriptor: Xylose isomerase
Authors:Kovalevsky, A.Y, Langan, P.
Deposit date:2009-10-21
Release date:2010-09-29
Last modified:2024-04-03
Method:NEUTRON DIFFRACTION (1.8 Å), X-RAY DIFFRACTION
Cite:Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values
Angew.Chem.Int.Ed.Engl., 50, 2011
3KBJ
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BU of 3kbj by Molmil
Room temperature X-ray structure of apo-D-Xylose Isomerase
Descriptor: Xylose isomerase
Authors:Kovalevsky, A.Y, Hanson, L, Langan, P.
Deposit date:2009-10-20
Release date:2010-09-29
Last modified:2024-02-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values.
Angew.Chem.Int.Ed.Engl., 50, 2011
6PU8
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BU of 6pu8 by Molmil
Room temperature X-ray structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate of keto-darunavir
Descriptor: (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3,3-dihydroxy-1-phenylbutan-2-yl]carbamate, HIV-1 protease
Authors:Kovalevsky, A, Das, A.
Deposit date:2019-07-17
Release date:2020-06-24
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design.
Acs Omega, 5, 2020
6PTP
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BU of 6ptp by Molmil
Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with tetrahedral intermediate mimic KVS-1
Descriptor: HIV-1 Protease, N~2~-[(2R,5S)-5-({(2S,3S)-2-[(N-acetyl-L-threonyl)amino]-3-methylpent-4-enoyl}amino)-2-butyl-4,4-dihydroxynonanoyl]-L-glutaminyl-L-argininamide
Authors:Kovalevsky, A, Das, A.
Deposit date:2019-07-16
Release date:2020-06-10
Last modified:2023-10-25
Method:NEUTRON DIFFRACTION (1.85 Å), X-RAY DIFFRACTION
Cite:Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design.
Acs Omega, 5, 2020
3B7V
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BU of 3b7v by Molmil
HIV-1 protease complexed with gem-diol-amine tetrahedral intermediate NLLTQI
Descriptor: CHLORIDE ION, GLYCEROL, Protease, ...
Authors:Kovalevsky, A.Y, Chumanevich, A.A, Weber, I.T.
Deposit date:2007-10-31
Release date:2007-12-18
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (1.46 Å)
Cite:Caught in the Act: The 1.5 A Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate.
Biochemistry, 46, 2007
8V8G
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BU of 8v8g by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-196) in complex with ensitrelvir (ESV)
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Kovalevsky, A, Coates, L.
Deposit date:2023-12-05
Release date:2024-05-29
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease.
J.Mol.Biol., 436, 2024
8V7T
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BU of 8v7t by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-199)
Descriptor: Non-structural protein 7
Authors:Kovalevsky, A, Coates, L.
Deposit date:2023-12-04
Release date:2024-05-29
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease.
J.Mol.Biol., 436, 2024
8V8E
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BU of 8v8e by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain (residues 1-199-6H) in complex with ensitrelvir (ESV)
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, peptide
Authors:Kovalevsky, A, Coates, L.
Deposit date:2023-12-05
Release date:2024-05-29
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (2 Å)
Cite:Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease.
J.Mol.Biol., 436, 2024
8V7W
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BU of 8v7w by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease catalytic domain C145A precursor, residues nsp4(-6)-1-199-6H
Descriptor: Replicase polyprotein 1ab
Authors:Kovalevsky, A, Coates, L.
Deposit date:2023-12-04
Release date:2024-05-29
Last modified:2024-06-12
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease.
J.Mol.Biol., 436, 2024
2F80
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BU of 2f80 by Molmil
HIV-1 Protease mutant D30N complexed with inhibitor TMC114
Descriptor: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE, CHLORIDE ION, POL POLYPROTEIN, ...
Authors:Kovalevsky, A.Y, Weber, I.T.
Deposit date:2005-12-01
Release date:2006-03-07
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Effectiveness of Nonpeptide Clinical Inhibitor TMC-114 on HIV-1 Protease with Highly Drug Resistant Mutations D30N, I50V, and L90M.
J.Med.Chem., 49, 2006
2F8G
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BU of 2f8g by Molmil
HIV-1 protease mutant I50V complexed with inhibitor TMC114
Descriptor: (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE, ACETIC ACID, CHLORIDE ION, ...
Authors:Kovalevsky, A.Y, Weber, I.T.
Deposit date:2005-12-02
Release date:2006-03-07
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (1.22 Å)
Cite:Effectiveness of Nonpeptide Clinical Inhibitor TMC-114 on HIV-1 Protease with Highly Drug Resistant Mutations D30N, I50V, and L90M.
J.Med.Chem., 49, 2006
8DT4
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BU of 8dt4 by Molmil
X-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime MMB4 (POX-hAChE-MMB4)
Descriptor: 1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium}, Acetylcholinesterase, DIETHYL PHOSPHONATE, ...
Authors:Kovalevsky, A.Y, Gerlits, O, Radic, Z.
Deposit date:2022-07-25
Release date:2022-11-02
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering.
Structure, 30, 2022

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