9nwb

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-280-5I

Method: X-RAY DIFFRACTION D_max: 60.7 Å Quality: REASONABLE

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	9nwb
沉积日期 deposition_date	2025-03-21
结构标题 title	Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-280-5I
关键词 keywords	SARS-CoV-2 main protease, 3C-like proteinase, VIRAL PROTEIN, SARS-CoV-2; 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	22.26 Å
回转半径 Rg (电子) rg_electron	21.66 Å
零角强度 I(0) i0	39107100.00
分子量 molecular_weight	32170.0 kDa
排除体积 excluded_volume	30934 Å³
包络体积 envelope_volume	49762 Å³
水化壳体积 shell_volume	19992 Å³
包络直径 envelope_diameter	79.7 Å
壳层 Rg shell_rg	27.54 Å
包络 Rg envelope_rg	21.97 Å
形状 Rg shape_rg	21.65 Å
总 Rg total_rg	22.21 Å
总原子数 total_atoms	2412
残基数 n_residues	306
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	60.7 Å
Rg (实空间) rg_real	21.41 Å
Rg 误差 (实空间) rg_real_error	0.10 Å
I(0) (实空间) i0_real	3.7470e+07
I(0) 误差 (实空间) i0_real_error	3.4900e+05
Rg (倒空间) rg_reciprocal	22.34 Å
I(0) (倒空间) i0_reciprocal	39110000.0000
解质量估计 total_estimate	0.6795
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	23.0 Å
偏度 Skewness skewness	0.401
峰度 Kurtosis kurtosis	-0.473
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	3.5960
最高正则化参数 α highest_alpha	9405000.0000
实空间数据点数 n_real_points	67
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 0.982; Sysdev: 0.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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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	ORF1a polyprotein
分子量 formula_weight	33825.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2436

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

来源 Source

来源生物 organism	Severe acute respiratory syndrome coronavirus
NCBI 分类编号 ncbi_taxonomy_id	2901879
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;(1R,2S,5S)-N-{(1S,2R)-1-hydroxy-1-(5-iodo-1,3-benzothiazol-2-yl)-3-[(3R)-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	763.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	24

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7. 引用文献 (1)

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晶胞边长 a length_a	45.412 Å
晶胞边长 b length_b	64.071 Å
晶胞边长 c length_c	104.988 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	4

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.010 Å
最低分辨率 resolution_low	41.710 Å
R 因子 r_factor	0.2097
R_work r_work	0.2076
R_free r_free	0.2485

fit	/app/data/saxs_computation/nw/9nwb/9nwb.fit
pddf	/app/data/pr_computation/nw/9nwb/9nwb.pr.out
profile	/app/data/saxs_computation/nw/9nwb/9nwb.dat

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-280-5I

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