8eyj

Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with Nirmatrelvir

Method: X-RAY DIFFRACTION D_max: 83.0 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	8eyj
沉积日期 deposition_date	2022-10-27
结构标题 title	Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with Nirmatrelvir
关键词 keywords	Main Protease, complex, Nirmatrelvir, VIRAL PROTEIN; VIRAL PROTEIN
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	26.55 Å
回转半径 Rg (电子) rg_electron	25.54 Å
零角强度 I(0) i0	76795500.00
分子量 molecular_weight	67828.0 kDa
排除体积 excluded_volume	84502 Å³
包络体积 envelope_volume	100680 Å³
水化壳体积 shell_volume	32564 Å³
包络直径 envelope_diameter	86.8 Å
壳层 Rg shell_rg	33.17 Å
包络 Rg envelope_rg	25.63 Å
形状 Rg shape_rg	25.52 Å
总 Rg total_rg	26.40 Å
总原子数 total_atoms	9410
残基数 n_residues	606
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	83.0 Å
Rg (实空间) rg_real	26.42 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	7.6800e+07
I(0) 误差 (实空间) i0_real_error	1.1170e+06
Rg (倒空间) rg_reciprocal	26.46 Å
I(0) (倒空间) i0_reciprocal	76800000.0000
解质量估计 total_estimate	0.9057
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	34.6 Å
偏度 Skewness skewness	0.148
峰度 Kurtosis kurtosis	-0.551
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	39320000.0000
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: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.967

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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	33937.6 kDa
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	10168

QSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSSGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus 2
NCBI 分类编号 ncbi_taxonomy_id	2697049
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;(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 ;
分子量 formula_weight	501.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	713

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8eyjA01
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	8eyjA02
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	8eyjB01
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	8eyjB02
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	67.646 Å
晶胞边长 b length_b	101.969 Å
晶胞边长 c length_c	103.626 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.738 Å
最低分辨率 resolution_low	72.788 Å
R 因子 r_factor	—
R_work r_work	0.1931
R_free r_free	0.2339

fit	/app/data/saxs_computation/ey/8eyj/8eyj.fit
pddf	/app/data/pr_computation/ey/8eyj/8eyj.pr.out
profile	/app/data/saxs_computation/ey/8eyj/8eyj.dat

Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with Nirmatrelvir

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