SAXSdb — 2d2d

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2d2d
沉积日期 deposition_date	2005-09-08
结构标题 title	Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor I2
关键词 keywords	Anti-parallel B-barrel, anti-parallel A-helices, Hydrolase; HYDROLASE
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	25.97 Å
回转半径 Rg (电子) rg_electron	24.99 Å
零角强度 I(0) i0	75999300.00
分子量 molecular_weight	67773.0 kDa
排除体积 excluded_volume	84562 Å³
包络体积 envelope_volume	96389 Å³
水化壳体积 shell_volume	31773 Å³
包络直径 envelope_diameter	85.0 Å
壳层 Rg shell_rg	32.58 Å
包络 Rg envelope_rg	25.11 Å
形状 Rg shape_rg	24.97 Å
总 Rg total_rg	25.83 Å
总原子数 total_atoms	4749
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	81.2 Å
Rg (实空间) rg_real	26.20 Å
Rg 误差 (实空间) rg_real_error	0.15 Å
I(0) (实空间) i0_real	7.4440e+07
I(0) 误差 (实空间) i0_real_error	6.9520e+05
Rg (倒空间) rg_reciprocal	25.88 Å
I(0) (倒空间) i0_reciprocal	76000000.0000
解质量估计 total_estimate	0.7040
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.3 Å
偏度 Skewness skewness	0.210
峰度 Kurtosis kurtosis	-0.437
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	6.0820
最高正则化参数 α highest_alpha	37930000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 0.925; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.566

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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
分子量 formula_weight	34288.1 kDa
EC 编号 ec_number	3.4.24.-
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	4885

GPLGSSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ

来源 Source

来源生物 organism	SARS coronavirus
NCBI 分类编号 ncbi_taxonomy_id	227859
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	;ETHYL (2E,4S)-4-[((2R)-2-{[N-(TERT-BUTOXYCARBONYL)-L-VALYL]AMINO}-2-PHENYLETHANOYL)AMINO]-5-[(3S)-2-OXOPYRROLIDIN-3-YL]PENT-2-ENOATE ;
分子量 formula_weight	558.7 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	136

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2d2da_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

结构域编号 domain_id	d2d2db_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.47 — Trypsin-like serine proteases
超家族 Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
家族 Family family	b.47.1.4 — Viral cysteine protease of trypsin fold

CATH v4.4 (6 domains)

结构域编号 domain_id	2d2dA01
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	2d2dA02
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	2d2dA03
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	2d2dB01
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	2d2dB02
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	2d2dB03
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	50.703 Å
晶胞边长 b length_b	94.737 Å
晶胞边长 c length_c	66.204 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	103.04 °
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	2.700 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2090
R_free r_free	0.2820

fit	/app/data/saxs_computation/d2/2d2d/2d2d.fit
pddf	/app/data/pr_computation/d2/2d2d/2d2d.pr.out
profile	/app/data/saxs_computation/d2/2d2d/2d2d.dat

Crystal Structure Of SARS-CoV Mpro in Complex with an Inhibitor I2

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