8fiw

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10221

Method: X-RAY DIFFRACTION D_max: 83.2 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8fiw
沉积日期 deposition_date	2022-12-16
结构标题 title	Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10221
关键词 keywords	SARS-CoV-2 Mpro, Main protease, VIRAL PROTEIN, HYDROLASE-INHIBITOR complex; VIRAL PROTEIN, HYDROLASE/INHIBITOR
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	26.56 Å
回转半径 Rg (电子) rg_electron	25.56 Å
零角强度 I(0) i0	75089700.00
分子量 molecular_weight	67221.0 kDa
排除体积 excluded_volume	83840 Å³
包络体积 envelope_volume	101060 Å³
水化壳体积 shell_volume	32562 Å³
包络直径 envelope_diameter	86.4 Å
壳层 Rg shell_rg	33.12 Å
包络 Rg envelope_rg	25.73 Å
形状 Rg shape_rg	25.54 Å
总 Rg total_rg	26.42 Å
总原子数 total_atoms	4714
残基数 n_residues	603
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	83.2 Å
Rg (实空间) rg_real	26.43 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	7.5090e+07
I(0) 误差 (实空间) i0_real_error	1.0330e+06
Rg (倒空间) rg_reciprocal	26.47 Å
I(0) (倒空间) i0_reciprocal	75090000.0000
解质量估计 total_estimate	0.9066
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	80.5 Å
偏度 Skewness skewness	0.155
峰度 Kurtosis kurtosis	-0.541
角度范围 angular_range	— – 0.3000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	45970000.0000
实空间数据点数 n_real_points	61
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.997

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	3C-like proteinase nsp5
分子量 formula_weight	33825.5 kDa
EC 编号 ec_number	3.4.22.69
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	4749

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
通用名 common_name	2019-nCoV, SARS-CoV-2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

描述 description	N-([1,1'-biphenyl]-4-yl)-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]prop-2-enamide
分子量 formula_weight	461.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	N-([1,1'-biphenyl]-4-yl)-N-[(1S)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]prop-2-enamide
分子量 formula_weight	461.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	8fiwA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	10 — Trypsin-like serine proteases

结构域编号 domain_id	8fiwA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1840 — main proteinase (3clpro) structure, domain 3
同源超家族 H-superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

结构域编号 domain_id	8fiwB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	1840 — main proteinase (3clpro) structure, domain 3
同源超家族 H-superfamily homologous superfamily	10 — main proteinase (3clpro) structure, domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	45.160 Å
晶胞边长 b length_b	53.355 Å
晶胞边长 c length_c	114.462 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.67 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.540 Å
最低分辨率 resolution_low	48.250 Å
R 因子 r_factor	0.2203
R_work r_work	0.2182
R_free r_free	0.2627

fit	/app/data/saxs_computation/fi/8fiw/8fiw.fit
pddf	/app/data/pr_computation/fi/8fiw/8fiw.pr.out
profile	/app/data/saxs_computation/fi/8fiw/8fiw.dat

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun10221

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction