9n6f

X-ray structure of SARS-CoV-2 main protease M165I covalently bound to inhibitor GRL-051-22 at 1.90 A

Method: X-RAY DIFFRACTION D_max: 76.4 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	9n6f
沉积日期 deposition_date	2025-02-05
结构标题 title	X-ray structure of SARS-CoV-2 main protease M165I covalently bound to inhibitor GRL-051-22 at 1.90 A
关键词 keywords	;Main protease, 3-chymotrypsin-like protease, Mpro, 3CLpro, Mutant, VIRAL PROTEIN, Structural Genomics, Center for Structural Biology of Infectious Diseases, CSBID ;; 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	22.52 Å
回转半径 Rg (电子) rg_electron	21.75 Å
零角强度 I(0) i0	21195600.00
分子量 molecular_weight	34191.0 kDa
排除体积 excluded_volume	42235 Å³
包络体积 envelope_volume	49957 Å³
水化壳体积 shell_volume	20033 Å³
包络直径 envelope_diameter	79.4 Å
壳层 Rg shell_rg	27.62 Å
包络 Rg envelope_rg	21.97 Å
形状 Rg shape_rg	21.78 Å
总 Rg total_rg	22.40 Å
总原子数 total_atoms	4618
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	76.4 Å
Rg (实空间) rg_real	22.61 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	2.1200e+07
I(0) 误差 (实空间) i0_real_error	3.0520e+05
Rg (倒空间) rg_reciprocal	22.59 Å
I(0) (倒空间) i0_reciprocal	21200000.0000
解质量估计 total_estimate	0.5970
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	75.3 Å
偏度 Skewness skewness	0.480
峰度 Kurtosis kurtosis	-0.311
角度范围 angular_range	— – 0.3550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	8768000.0000
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: 0.757; Stabil: 0.999; Sysdev: 0.189; Positv: 1.000; Valcen: 0.920; 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 (4)

Entity 1 polymer

描述 description	3C-like proteinase nsp5
分子量 formula_weight	33807.5 kDa
EC 编号 ec_number	3.4.22.69
突变 mutation	M165I
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	5209

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHIELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ

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	;(3S)-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-2-[3-methyl-N-(trifluoroacetyl)-L-valyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxamide ;
分子量 formula_weight	523.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	287

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7. 引用文献 (2)

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晶胞边长 a length_a	97.112 Å
晶胞边长 b length_b	81.915 Å
晶胞边长 c length_c	54.337 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	117.31 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	monoclinic

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	18.030 Å
R 因子 r_factor	0.1651
R_work r_work	0.1615
R_free r_free	0.2156

fit	/app/data/saxs_computation/n6/9n6f/9n6f.fit
pddf	/app/data/pr_computation/n6/9n6f/9n6f.pr.out
profile	/app/data/saxs_computation/n6/9n6f/9n6f.dat

X-ray structure of SARS-CoV-2 main protease M165I covalently bound to inhibitor GRL-051-22 at 1.90 A

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