2h43

Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide

Method: X-RAY DIFFRACTION D_max: 219.4 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	2h43
沉积日期 deposition_date	2006-05-23
结构标题 title	Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide
关键词 keywords	knob-hole interaction, fragment D, coiled-coil, BLOOD CLOTTING; BLOOD CLOTTING
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	55.36 Å
回转半径 Rg (电子) rg_electron	57.21 Å
零角强度 I(0) i0	369623000.00
分子量 molecular_weight	153310.0 kDa
排除体积 excluded_volume	189390 Å³
包络体积 envelope_volume	252920 Å³
水化壳体积 shell_volume	45042 Å³
包络直径 envelope_diameter	232.5 Å
壳层 Rg shell_rg	43.77 Å
包络 Rg envelope_rg	58.58 Å
形状 Rg shape_rg	57.09 Å
总 Rg total_rg	57.13 Å
总原子数 total_atoms	10770
残基数 n_residues	1331
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	219.4 Å
Rg (实空间) rg_real	56.60 Å
Rg 误差 (实空间) rg_real_error	5.55 Å
I(0) (实空间) i0_real	3.6960e+08
I(0) 误差 (实空间) i0_real_error	9.6390e+06
Rg (倒空间) rg_reciprocal	54.34 Å
I(0) (倒空间) i0_reciprocal	368400000.0000
解质量估计 total_estimate	0.6424
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	31.3 Å
偏度 Skewness skewness	0.732
峰度 Kurtosis kurtosis	-0.152
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10860000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.153; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.065; Smooth: 0.828

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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	Fibrinogen alpha chain
分子量 formula_weight	10245.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,D
原子数 atom_count	10770

VSEDLRSRIEVLKRKVIEKVQHIQLLQKNVRAQLVDMKRLEVDIDIKIRSCRGSCSRALAREVDLKDYEDQQKQLEQVIAKDLLPSR

Entity 2 polymer

描述 description	Fibrinogen beta chain
分子量 formula_weight	37692.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

DNENVVNEYSSELEKHQLYIDETVNSNIPTNLRVLRSILENLRSKIQKLESDVSAQMEYCRTPCTVSCNIPVVSGKECEEIIRKGGETSEMYLIQPDSSVKPYRVYCDMNTENGGWTVIQNRQDGSVDFGRKWDPYKQGFGNVATNTDGKNYCGLPGEYWLGNDKISQLTRMGPTELLIEMEDWKGDKVKAHYGGFTVQNEANKYQISVNKYRGTAGNALMDGASQLMGENRTMTIHNGMFFSTYDRDNDGWLTSDPRKQCSKEDGGGWWYNRCHAANPNGRYYWGGQYTWDMAKHGTDDGVVWMNWKGSWYSMRKMSMKIRPFFPQQ

Entity 3 polymer

描述 description	Fibrinogen gamma chain
分子量 formula_weight	36564.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

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

MLEEIMKYEASILTHDSSIRYLQEIYNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQDIANKGAKQSGLYFIKPLKANQQFLVYCEIDGSGNGWTVFQKRLDGSVDFKKNWIQYKEGFGHLSPTGTTEFWLGNEKIHLISTQSAIPYALRVELEDWNGRTSTADYAMFKVGPEADKYRLTYAYFAGGDAGDAFDGFDFGDDPSDKFFTSHNGMQFSTWDNDNDKFEGNCAEQDGSGWWMNKCHAGHLNGVYYQGGTYSKASTPNGYDNGIIWATWKTRWYSMKKTTMKIIPFNRLTIGEGQQHHLGGAKQAGDV

Entity 4 polymer

描述 description	GLY-HIS-ARG-PRO-AMIDE peptide ligand
分子量 formula_weight	479.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I,J

AHRPX

Entity 5 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 6 branched

描述 description	2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d2h43a1
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

结构域编号 domain_id	d2h43d1
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.8 — Fibrinogen coiled-coil and central regions
家族 Family family	h.1.8.1 — Fibrinogen coiled-coil and central regions

CATH v4.4 (10 domains)

结构域编号 domain_id	2h43A00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2h43B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	2h43B02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	2h43C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	2h43C02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	2h43D00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily	50 —

结构域编号 domain_id	2h43E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	2h43E02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

结构域编号 domain_id	2h43F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	215 — Gamma Fibrinogen; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Gamma Fibrinogen, chain A, domain 1

结构域编号 domain_id	2h43F02
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	530 — Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2

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7. 引用文献 (1)

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晶胞边长 a length_a	105.000 Å
晶胞边长 b length_b	47.900 Å
晶胞边长 c length_c	171.400 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.41 °
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	0.2440
R_work r_work	0.2510
R_free r_free	0.3070

fit	/app/data/saxs_computation/h4/2h43/2h43.fit
pddf	/app/data/pr_computation/h4/2h43/2h43.pr.out
profile	/app/data/saxs_computation/h4/2h43/2h43.dat

Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide

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 polymer

聚合体 Polymer

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (2 domains)

CATH v4.4 (10 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)