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新型コロナウイルスの構造情報

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コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症(Novel Coronavirus disease 2019: COVID-19)の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)を理解し有効な薬を開発するため,関連するタンパク質の構造研究は既に始まっています。そして,解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため,新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは,同じ著者によるグループ登録のエントリーも全て区別し,すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており,アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは,今週公開された最も新しいエントリーです。


作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
9F7A
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BU of 9f7a by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P80R
分子名称: Nucleoprotein, ZINC ION
著者Dhamotharan, K, Schlundt, A.
登録日2024-05-03
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F7C
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BU of 9f7c by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I
分子名称: Nucleoprotein, ZINC ION
著者Dhamotharan, K, Schlundt, A.
登録日2024-05-03
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9F83
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BU of 9f83 by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A, Guenther, S.
登録日2024-05-06
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9FBG
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BU of 9fbg by Molmil
SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P151S
分子名称: Nucleoprotein
著者Dhamotharan, K, Schlundt, A.
登録日2024-05-13
公開日2024-11-20
最終更新日2024-12-18
実験手法X-RAY DIFFRACTION (2.54 Å)
主引用文献A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Nat Commun, 15, 2024
9GWO
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BU of 9gwo by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571126
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-27
公開日2024-11-20
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8RJ7
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BU of 8rj7 by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Camel-derived nanobody 1.29, LYSINE, ...
著者Casasnovas, J.M, Fernandez, L.A, Silva, K.
登録日2023-12-20
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29
To Be Published
8YKJ
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BU of 8ykj by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with X77
分子名称: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide, Non-structural protein 11
著者Zhou, X.L, Lin, C, Li, W.W, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.99 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKM
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BU of 8ykm by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with X77
分子名称: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
著者Zeng, P, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.84 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKN
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Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with X77
分子名称: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide, Non-structural protein 11
著者Wang, J, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.77 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKO
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BU of 8yko by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex withX77
分子名称: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
著者Li, W.W, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2.11 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKP
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BU of 8ykp by Molmil
Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with X77
分子名称: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
著者Zou, X.F, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2.4 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
8YKQ
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BU of 8ykq by Molmil
Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with X77
分子名称: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
著者Zou, X.F, Zhang, J, Li, J.
登録日2024-03-05
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Int.J.Biol.Macromol., 276, 2024
9CRC
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BU of 9crc by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 3 closed RBDs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Croll, T.I, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRD
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BU of 9crd by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 1 open RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Croll, T.I, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRE
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BU of 9cre by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 3 closed RBDs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Croll, T.I, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRF
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BU of 9crf by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 1 open RBD
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Croll, T.I, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (4 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRG
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BU of 9crg by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed RBDs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Kotecha, A, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.3 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRH
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BU of 9crh by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9CRI
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BU of 9cri by Molmil
Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed RBDs
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-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, ...
著者Ke, Z, Briggs, J.A.G.
登録日2024-07-22
公開日2024-11-27
最終更新日2024-12-25
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants.
Embo J., 43, 2024
9HBQ
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BU of 9hbq by Molmil
SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide
分子名称: (1~{R})-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
著者Hanoulle, X, Charton, J, Deprez, B.
登録日2024-11-08
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.795 Å)
主引用文献SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-indane-1-carboxamide
To Be Published
9HC1
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BU of 9hc1 by Molmil
SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide
分子名称: (1~{R})-~{N}-(3-chlorophenyl)-3-oxidanylidene-~{N}-[4-(2-oxidanylidenepyrrolidin-1-yl)phenyl]-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
著者Hanoulle, X, Charton, J, Deprez, B.
登録日2024-11-08
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.493 Å)
主引用文献SARS-CoV-2 Main Protease complexed with (1R)-N-(3-chlorophenyl)-3-oxo-N-[4-(2-oxopyrrolidin-1-yl)phenyl]indane-1-carboxamide
To Be Published
9HD8
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BU of 9hd8 by Molmil
SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
分子名称: (1~{R})-~{N}-[4-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]phenyl]-~{N}-(3-chlorophenyl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5, SODIUM ION
著者Hanoulle, X, Charton, J, Deprez, B.
登録日2024-11-12
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.696 Å)
主引用文献SARS-CoV-2 Main Protease in complex with with (1R)-N-(3-chlorophenyl)-N-[4-(2,4-dioxo-1H-pyrimidin-5-yl)phenyl]-3-oxo-indane-1-carboxamide
To Be Published
9HDC
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BU of 9hdc by Molmil
SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one
分子名称: (3~{S})-3-[(3~{R})-3-phenylpiperidin-1-yl]carbonyl-2,3-dihydroinden-1-one, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
著者Hanoulle, X, Charton, J, Deprez, B.
登録日2024-11-12
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.794 Å)
主引用文献SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one
To Be Published
9HDJ
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BU of 9hdj by Molmil
SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
分子名称: (3~{R})-3-[(3~{R})-3-phenyl-4-(phenylmethyl)piperazin-1-yl]carbonyl-2,3-dihydroinden-1-one, 3C-like proteinase nsp5, FORMIC ACID
著者Hanoulle, X, Charton, J, Deprez, B.
登録日2024-11-12
公開日2024-11-27
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献SARS-CoV-2 Main Protease in complex with (3R)-3-[(3R)-4-benzyl-3-phenyl-piperidine-1-carbonyl]indan-1-one
To Be Published
9HDN
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BU of 9hdn by Molmil
SARS-CoV-2 Main Protease in complex with (1R)-3-oxo-N-[2-oxo-2-(N-phenylanilino)ethyl]indane-1-carboxamide
分子名称: (1~{R})-~{N}-[2-(diphenylamino)-2-oxidanylidene-ethyl]-3-oxidanylidene-1,2-dihydroindene-1-carboxamide, 3C-like proteinase nsp5
著者Hanoulle, X, Charton, J, Deprez, B.
登録日2024-11-12
公開日2024-11-27
実験手法X-RAY DIFFRACTION (1.77 Å)
主引用文献SARS-CoV-2 Main Protease in complex with (1R)-3-oxo-N-[2-oxo-2-(N-phenylanilino)ethyl]indane-1-carboxamide
To Be Published

238582

件を2025-07-09に公開中

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