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신종 코로나바이러스 특집 콘텐츠

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코로나 바이러스
코로나 바이러스, 2020. David S. Goodsell @ RCSB PDB에 의한 오리지널 일러스트를 수정

신종 코로나바이러스 감염증 (Novel Coronavirus disease 2019:COVID-19)의 확산이 세계적으로 매우 큰 문제가 되고 있습니다. 시급히 새로운 바이러스(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)를 이해하고 효과적인 약을 개발하기 위해, 신속하게 구조 생물학 연구가 시작되고 있습니다. PDBj는 사용자의 편의를 도모하기 위해 신종 코로나바이러스의 특집 페이지를 제공하고 있습니다. 매주 수요일에 최신 항목이 추가됩니다.

바이러스 단백질에 관한 해설기사는 아래의 「이달의 분자」 페이지를 참조하십시오.

「전체 엔트리」 탭에는, 모든 PDB ID가 포함되어 있습니다. 이용자가 전체의 독립된 엔트리를 검색하고 싶을 때 사용하실 수 있으며, 동일 저자에 의한 그룹등록의 엔트리도 전부 구별되어 있습니다. 「대표구조」 탭에는, 분해능이 가장 높은 대표구조만을 표지하고 있습니다. 아미노산 서열이 100 % 일치하는 PDB 엔트리의 경우, 다른 리간드를 포함하여도 대표구조에는 제외됩니다. 「최신 엔트리」 탭은, 이번주 공개된 가장 최근의 엔트리 입니다.


Created: 2020-09-03 (last edited: more than 1 year ago)2022-09-02
8WGW
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BU of 8wgw by Molmil
Local refinement of RBD-ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:Wei, X, Zhang, Z.
Deposit date:2023-09-22
Release date:2024-02-28
Last modified:2024-04-24
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:The receptor binding domain of SARS-CoV-2 Omicron subvariants targets Siglec-9 to decrease its immunogenicity by preventing macrophage phagocytosis.
Nat.Immunol., 25, 2024
8YA5
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BU of 8ya5 by Molmil
Mpro from SARS-CoV-2
Descriptor: 3C-like proteinase
Authors:Zhang, C.Y, Xu, Q, Wang, W.W, Zhou, H, Wang, Q.S.
Deposit date:2024-02-07
Release date:2024-02-28
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:Crystallographic data collection using a multilayer monochromator on an undulator beamline at SSRF
To Be Published
8IG4
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BU of 8ig4 by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with GC376
Descriptor: Non-structural protein 11, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Zhou, X.L, Zhang, J, Li, J.
Deposit date:2023-02-20
Release date:2024-03-06
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.
J.Mol.Biol., 436, 2024
8IG7
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BU of 8ig7 by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Zeng, P, Zhang, J, Li, J.
Deposit date:2023-02-20
Release date:2024-03-06
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.
J.Mol.Biol., 436, 2024
8IG8
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BU of 8ig8 by Molmil
Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Zeng, X.Y, Zhang, J, Li, J.
Deposit date:2023-02-20
Release date:2024-03-06
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.
J.Mol.Biol., 436, 2024
8IG9
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BU of 8ig9 by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Zou, X.F, Zhang, J, Li, J.
Deposit date:2023-02-20
Release date:2024-03-06
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.
J.Mol.Biol., 436, 2024
8IGA
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BU of 8iga by Molmil
Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Wang, J, Zhang, J, Li, J.
Deposit date:2023-02-20
Release date:2024-03-06
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.63 Å)
Cite:Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.
J.Mol.Biol., 436, 2024
8IGB
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BU of 8igb by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Li, W.W, Zhang, J, Li, J.
Deposit date:2023-02-20
Release date:2024-03-06
Last modified:2024-05-08
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:Structural Basis for Coronaviral Main Proteases Inhibition by the 3CLpro Inhibitor GC376.
J.Mol.Biol., 436, 2024
8QO5
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BU of 8qo5 by Molmil
Conserved Structures and Dynamics in 5-Proximal Regions of Betacoronavirus RNA Genomes
Descriptor: SARS-CoV-2-SL5
Authors:Moura, T.R, Purta, E, Bernat, A, Baulin, E, Mukherjee, S, Bujnicki, J.M.
Deposit date:2023-09-28
Release date:2024-03-06
Last modified:2024-04-24
Method:ELECTRON MICROSCOPY (6.5 Å)
Cite:Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes.
Nucleic Acids Res., 52, 2024
8UPS
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BU of 8ups by Molmil
Structure of SARS-Cov2 3CLPro in complex with Compound 5
Descriptor: (1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, PHOSPHATE ION
Authors:Wu, Y, Qiang, D, Zhuang, N, Krishnamurthy, H, Klein, D.J.
Deposit date:2023-10-23
Release date:2024-03-06
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.44 Å)
Cite:Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
J.Med.Chem., 67, 2024
8UPV
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BU of 8upv by Molmil
Structure of SARS-Cov2 3CLPro in complex with Compound 33
Descriptor: 3C-like proteinase nsp5, methyl {(2S)-1-[(1S,3aR,6aS)-1-{[(2R,3S,6R)-6-fluoro-2-hydroxy-1-(methylamino)-1-oxoheptan-3-yl]carbamoyl}hexahydrocyclopenta[c]pyrrol-2(1H)-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate
Authors:Krishnamurthy, H, Zhuang, N, Qiang, D, Wu, Y, Klein, D.J.
Deposit date:2023-10-23
Release date:2024-03-06
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.57 Å)
Cite:Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
J.Med.Chem., 67, 2024
8UPW
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BU of 8upw by Molmil
Structure of SARS-Cov2 3CLPro in complex with Compound 34
Descriptor: 3C-like proteinase nsp5, methyl {(2S)-1-[(1S,3aR,6aS)-1-{[(2R,3S,6S)-6-fluoro-2-hydroxy-1-(methylamino)-1-oxoheptan-3-yl]carbamoyl}hexahydrocyclopenta[c]pyrrol-2(1H)-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate
Authors:Krishnamurthy, H, Zhuang, N, Qiang, D, Wu, Y, Klein, D.J.
Deposit date:2023-10-23
Release date:2024-03-06
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.44 Å)
Cite:Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
J.Med.Chem., 67, 2024
8UTE
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BU of 8ute by Molmil
Structure of SARS-Cov2 3CLPro in complex with Compound 27
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, methyl {(2S)-1-[(1S,3aR,6aS)-1-{[(2R,3S)-6,6-difluoro-2-hydroxy-1-(methylamino)-1-oxoheptan-3-yl]carbamoyl}hexahydrocyclopenta[c]pyrrol-2(1H)-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate
Authors:Krishnamurthy, H, Zhuang, N, Qiang, D, Wu, Y, Klein, D.J.
Deposit date:2023-10-31
Release date:2024-03-06
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
J.Med.Chem., 67, 2024
8XE9
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BU of 8xe9 by Molmil
XBB.1.5 RBD in complex with BD55-1205
Descriptor: BD55-1205 heavy chain, BD55-1205 light chain, Spike protein S2'
Authors:Feng, L.L.
Deposit date:2023-12-11
Release date:2024-03-06
Last modified:2024-04-24
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:XBB.1.5 RBD in complex with BD55-1205
To Be Published
8GDR
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BU of 8gdr by Molmil
SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Monoclonal antibody 002-S21B10 heavy chain variable domain, ...
Authors:Patel, A, Ortlund, E.A.
Deposit date:2023-03-06
Release date:2024-03-13
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Elucidating the mechanism of SARS-CoV-2 Omicron variant escape from a RBD class-3 human antibody
To Be Published
8INQ
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BU of 8inq by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant
Descriptor: 3C-like proteinase
Authors:Lin, M, Liu, X.
Deposit date:2023-03-10
Release date:2024-03-13
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant
To Be Published
8INT
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BU of 8int by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant
Descriptor: 3C-like proteinase
Authors:Lin, M, Liu, X.
Deposit date:2023-03-10
Release date:2024-03-13
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant
To Be Published
8INU
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BU of 8inu by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant in Complex with Inhibitor nirmatrelvir
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:Lin, M, Liu, X.
Deposit date:2023-03-10
Release date:2024-03-13
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant
To Be Published
8INW
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BU of 8inw by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor nirmatrelvir
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:Lin, M, Liu, X.
Deposit date:2023-03-10
Release date:2024-03-13
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor nirmatrelvir
To Be Published
8INX
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BU of 8inx by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant in Complex with Inhibitor ensitrelvir
Descriptor: 3C-like proteinase, 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:Lin, M, Liu, X.
Deposit date:2023-03-10
Release date:2024-03-13
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) G15S Mutant in Complex with Inhibitor ensitrelvir
To Be Published
8INY
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BU of 8iny by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor ensitrelvir
Descriptor: 3C-like proteinase, 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:Lin, M, Liu, X.
Deposit date:2023-03-10
Release date:2024-03-13
Method:X-RAY DIFFRACTION (1.59 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) K90R Mutant in Complex with Inhibitor ensitrelvir
To Be Published
8R1C
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BU of 8r1c by Molmil
SD1-2 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SD1-2 fab heavy chain, SD1-2 fab light chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2023-11-01
Release date:2024-03-13
Last modified:2024-04-10
Method:ELECTRON MICROSCOPY (2.2 Å)
Cite:The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86.
Nat Commun, 15, 2024
8SDF
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BU of 8sdf by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-04-06
Release date:2024-03-13
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Biorxiv, 2023
8SDG
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BU of 8sdg by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.43
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Neutralizing antibody CC25.43 heavy chain, Neutralizing antibody CC25.43 light chain, ...
Authors:Yuan, M, Wilson, I.A.
Deposit date:2023-04-06
Release date:2024-03-13
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.71 Å)
Cite:Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Biorxiv, 2023
8SIQ
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BU of 8siq by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibodies CC25.36 and CV38-142 Fab
Descriptor: CC25.36 Fab heavy chain, CC25.36 Fab light chain, CV38-142 Fab heavy chain, ...
Authors:Liu, H, Wilson, I.A.
Deposit date:2023-04-16
Release date:2024-03-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift
Biorxiv, 2023

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