SAXSdb — 1sr5

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1sr5
沉积日期 deposition_date	2004-03-22
结构标题 title	ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE
关键词 keywords	;SERINE PROTEINASE INHIBITOR, ANTITHROMBIN ACTIVATION BY HEP ANHYDROTHROMBIN, PROTEIN-PROTEIN INTERACTIONS, 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	33.24 Å
回转半径 Rg (电子) rg_electron	33.20 Å
零角强度 I(0) i0	95037000.00
分子量 molecular_weight	77722.0 kDa
排除体积 excluded_volume	97116 Å³
包络体积 envelope_volume	119260 Å³
水化壳体积 shell_volume	32051 Å³
包络直径 envelope_diameter	114.0 Å
壳层 Rg shell_rg	37.36 Å
包络 Rg envelope_rg	33.00 Å
形状 Rg shape_rg	33.19 Å
总 Rg total_rg	33.55 Å
总原子数 total_atoms	5459
残基数 n_residues	648
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	113.0 Å
Rg (实空间) rg_real	33.65 Å
Rg 误差 (实空间) rg_real_error	1.11 Å
I(0) (实空间) i0_real	9.5040e+07
I(0) 误差 (实空间) i0_real_error	1.7050e+06
Rg (倒空间) rg_reciprocal	33.48 Å
I(0) (倒空间) i0_reciprocal	95020000.0000
解质量估计 total_estimate	0.7978
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	28.2 Å
偏度 Skewness skewness	0.500
峰度 Kurtosis kurtosis	-0.570
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41680000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.629; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.617; Smooth: 0.865

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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 (7)

Entity 1 polymer

描述 description	Antithrombin-III
分子量 formula_weight	49101.0 kDa
来源方法 src_method	nat
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	5534

HGSPVDICTAKPRDIPMNPMCIYRSPEKKATEDEGSEQKIPEATNRRVWELSKANSRFATTFYQHLADSKNDNDNIFLSPLSISTAFAMTKLGACNDTLQQLMEVFKFDTISEKTSDQIHFFFAKLNCRLYRKANKSSKLVSANRLFGDKSLTFNETYQDISELVYGAKLQPLDFKENAEQSRAAINKWVSNKTEGRITDVIPSEAINELTVLVLVNTIYFKGLWKSKFSPENTRKELFYKADGESCSASMMYQEGKFRYRRVAEGTQVLELPFKGDDITMVLILPKPEKSLAKVEKELTPEVLQEWLDELEEMMLVVHMPRFRIEDGFSLKEQLQDMGLVDLFSPEKSKLPGIVAEGRDDLYVSDAFHKAFLEVNEEGSEAAASTAVVIAGRSLNPNRVTFKANRPFLVFIREVPLNTIIFMGRVANPCVK

Entity 2 polymer

描述 description	Prothrombin
分子量 formula_weight	4096.5 kDa
EC 编号 ec_number	3.4.21.5
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 3 polymer

描述 description	Prothrombin
分子量 formula_weight	29780.2 kDa
EC 编号 ec_number	3.4.21.5
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 4 branched

描述 description	;4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose-(1-4)-2,3,6-tri-O-methyl-beta-D-glucopyranose-(1-4)-2,3-di-O-methyl-6-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3R,4S,5S,6S)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol-(1-4)-2,3,6-tri-O-sulfo-alpha-D-glucopyranose-(1-4)-(2R,3R,4S,5S,6R)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol-(1-4)-1,5-anhydro-3-O-methyl-2,6-di-O-sulfo-D-glucitol ;
分子量 formula_weight	1815.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 5 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 6 non-polymer

描述 description	2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose
分子量 formula_weight	500.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 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	75

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1sr5.1
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.47.1.2 — Eukaryotic proteases

结构域编号 domain_id	d1sr5a_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.1 — Serpins
超家族 Superfamily superfamily	e.1.1 — Serpins
家族 Family family	e.1.1.1 — Serpins

CATH v4.4 (4 domains)

结构域编号 domain_id	1sr5A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	39 — Alpha-1-antitrypsin; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

结构域编号 domain_id	1sr5A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	497 — Antithrombin; Chain I, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

结构域编号 domain_id	1sr5C01
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	1sr5C02
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

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7. 引用文献 (1)

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晶胞边长 a length_a	90.040 Å
晶胞边长 b length_b	90.700 Å
晶胞边长 c length_c	159.900 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 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	—
R_work r_work	0.2270
R_free r_free	0.2780

fit	/app/data/saxs_computation/sr/1sr5/1sr5.fit
pddf	/app/data/pr_computation/sr/1sr5/1sr5.pr.out
profile	/app/data/saxs_computation/sr/1sr5/1sr5.dat

ANTITHROMBIN-ANHYDROTHROMBIN-HEPARIN TERNARY COMPLEX STRUCTURE

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

5. 实体与聚合体信息 (7)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 branched

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)