SAXSdb — 9cyd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9cyd
沉积日期 deposition_date	2024-08-02
结构标题 title	SARS-CoV-2 PLpro in complex with inhibitor WEHI-P4
关键词 keywords	SARS CoV-2, papain-like protease, COVID19, inhibitor, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/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	23.59 Å
回转半径 Rg (电子) rg_electron	22.76 Å
零角强度 I(0) i0	21345400.00
分子量 molecular_weight	35429.0 kDa
排除体积 excluded_volume	44371 Å³
包络体积 envelope_volume	52770 Å³
水化壳体积 shell_volume	20722 Å³
包络直径 envelope_diameter	87.8 Å
壳层 Rg shell_rg	28.27 Å
包络 Rg envelope_rg	23.26 Å
形状 Rg shape_rg	22.74 Å
总 Rg total_rg	23.54 Å
总原子数 total_atoms	4899
残基数 n_residues	309
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	84.2 Å
Rg (实空间) rg_real	23.76 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	2.1350e+07
I(0) 误差 (实空间) i0_real_error	3.5300e+05
Rg (倒空间) rg_reciprocal	23.72 Å
I(0) (倒空间) i0_reciprocal	21340000.0000
解质量估计 total_estimate	0.8335
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	23.7 Å
偏度 Skewness skewness	0.554
峰度 Kurtosis kurtosis	-0.035
角度范围 angular_range	— – 0.3350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	4121000.0000
实空间数据点数 n_real_points	65
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.773; Smooth: 0.965

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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	Papain-like protease
分子量 formula_weight	35927.7 kDa
EC 编号 ec_number	3.4.19.12
突变 mutation	C111S
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	4899

SNAEVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIK

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	(1S,4s)-4-{(3R)-3-[(E)-(methoxyimino)(6-methoxynaphthalen-2-yl)methyl]piperidin-1-yl}cyclohexan-1-ol
分子量 formula_weight	396.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (9)

A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID.

Nat Commun (2025)

PMID: 40180914 · DOI: 10.1038/s41467-025-57905-4 PRIMARY

;MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron. ;

J Synchrotron Radiat (2018)

PMID: 29714201 · DOI: 10.1107/S1600577518003120

CCP4i2: the new graphical user interface to the CCP4 program suite.

Acta Crystallogr D Struct Biol (2018)

PMID: 29533233 · DOI: 10.1107/S2059798317016035

An introduction to data reduction: space-group determination, scaling and intensity statistics.

Acta Crystallogr D Biol Crystallogr (2011)

PMID: 21460446 · DOI: 10.1107/S090744491003982X

XDS for crystallography

Acta Crystallogr D Biol Crystallogr (2010)

PMID: 20124692 · DOI: 10.1107/S0907444909047337

Features and development of Coot.

Acta Crystallogr D Biol Crystallogr (2010)

PMID: 20383002 · DOI: 10.1107/S0907444910007493

Phaser crystallographic software.

J Appl Crystallogr (2007)

PMID: 19461840 · DOI: 10.1107/S0021889807021206

Scaling and assessment of data quality.

Acta Crystallogr D Biol Crystallogr (2006)

PMID: 16369096 · DOI: 10.1107/S0907444905036693

Recent developments in the PHENIX software for automated crystallographic structure determination.

J Synchrotron Radiat (2004)

PMID: 14646133 · DOI: 10.1107/s0909049503024130

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晶胞边长 a length_a	156.584 Å
晶胞边长 b length_b	156.584 Å
晶胞边长 c length_c	156.584 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	24

空间群 space_group	P 43 3 2
空间群编号 int_tables_number	212
晶系 crystal_system	cubic

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	49.520 Å
R 因子 r_factor	0.2419
R_work r_work	0.2406
R_free r_free	0.2645

fit	/app/data/saxs_computation/cy/9cyd/9cyd.fit
pddf	/app/data/pr_computation/cy/9cyd/9cyd.pr.out
profile	/app/data/saxs_computation/cy/9cyd/9cyd.dat

SARS-CoV-2 PLpro in complex with inhibitor WEHI-P4

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