1fe8

CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING

Method: X-RAY DIFFRACTION D_max: 152.7 Å Quality: GOOD

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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1fe8
沉积日期 deposition_date	2000-07-21
结构标题 title	CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING
关键词 keywords	Collagen binding, conformational changes, epitope, von Willebrand factor A-type domain, IMMUNE SYSTEM; IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	42.74 Å
回转半径 Rg (电子) rg_electron	42.59 Å
零角强度 I(0) i0	610052000.00
分子量 molecular_weight	199490.0 kDa
排除体积 excluded_volume	248070 Å³
包络体积 envelope_volume	328980 Å³
水化壳体积 shell_volume	65947 Å³
包络直径 envelope_diameter	162.4 Å
壳层 Rg shell_rg	46.65 Å
包络 Rg envelope_rg	41.86 Å
形状 Rg shape_rg	42.56 Å
总 Rg total_rg	42.88 Å
总原子数 total_atoms	13994
残基数 n_residues	1822
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	152.7 Å
Rg (实空间) rg_real	42.84 Å
Rg 误差 (实空间) rg_real_error	1.84 Å
I(0) (实空间) i0_real	6.1010e+08
I(0) 误差 (实空间) i0_real_error	1.2030e+07
Rg (倒空间) rg_reciprocal	42.74 Å
I(0) (倒空间) i0_reciprocal	610000000.0000
解质量估计 total_estimate	0.8430
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	49.5 Å
偏度 Skewness skewness	0.479
峰度 Kurtosis kurtosis	0.059
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	55040000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.750

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (7)

Entity 1 polymer

描述 description	VON WILLEBRAND FACTOR
分子量 formula_weight	21025.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	14872

GSHMAPDCSQPLDVILLLDGSSSFPASYFDEMKSFAKAFISKANIGPRLTQVSVLQYGSITTIDVPWNVVPEKAHLLSLVDVMQREGGPSQIGDALGFAVRYLTSEMHGARPGASKAVVILVTDVSVDSVDAAADAARSNRVTVFPIGIGDRYDAAQLRILAGPAGDSNVVKLQRIEDLPTMVTLGNSFLHKLCSG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	IMMUNOGLOBULIN IGG RU5
分子量 formula_weight	22420.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

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

DVKLVQSGPGLVAPSQSLSITCTVSGFSLTTYGVSWVRQPPGKGLEWLGVIWGDGNTTYHSALISRLSISKDNSRSQVFLKLNSLHTDDTATYYCAGNYYGMDYWGQGTSVTVSSAETTAPSVYKLEPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG

Entity 3 polymer

描述 description	IMMUNOGLOBULIN IGG RU5
分子量 formula_weight	23192.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L,M,N

DIAMTQTTSSLSASLGQKVTISCRASQDIGNYLNWYQQKPDGTVRLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLESEDIATYFCQNGGTNPWTFGGGTKLEVKRADAAPTTSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Entity 4 branched

描述 description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	367.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

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	2

Entity 6 non-polymer

描述 description	CACODYLATE ION
分子量 formula_weight	137.0 kDa
来源方法 src_method	syn
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	878

▼

6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (15 domains)

结构域编号 domain_id	d1fe8a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.1 — Integrin A (or I) domain

结构域编号 domain_id	d1fe8b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.1 — Integrin A (or I) domain

结构域编号 domain_id	d1fe8c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.62 — vWA-like
超家族 Superfamily superfamily	c.62.1 — vWA-like
家族 Family family	c.62.1.1 — Integrin A (or I) domain

结构域编号 domain_id	d1fe8h1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fe8h2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fe8i1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fe8i2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fe8j1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fe8j2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fe8l1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fe8l2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fe8m1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fe8m2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

结构域编号 domain_id	d1fe8n1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.1 — V set domains (antibody variable domain-like)

结构域编号 domain_id	d1fe8n2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.1 — Immunoglobulin
家族 Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (15 domains)

结构域编号 domain_id	1fe8A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1fe8B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1fe8C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	410 — von Willebrand factor, type A domain

结构域编号 domain_id	1fe8H01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8H02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8I01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8I02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8J01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8J02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8L01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8L02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8M01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8M02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8N01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	1fe8N02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

▶

7. 引用文献 (4)

▶

晶胞边长 a length_a	121.800 Å
晶胞边长 b length_b	183.600 Å
晶胞边长 c length_c	131.800 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	116.20 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

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

分辨率 resolution	2.030 Å
最低分辨率 resolution_low	29.900 Å
R 因子 r_factor	0.2290
R_work r_work	0.2270
R_free r_free	0.2640

fit	/app/data/saxs_computation/fe/1fe8/1fe8.fit
pddf	/app/data/pr_computation/fe/1fe8/1fe8.pr.out
profile	/app/data/saxs_computation/fe/1fe8/1fe8.dat

CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING

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

来源 Source

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) 30 domains

SCOP 2.08 (15 domains)

CATH v4.4 (15 domains)

7. 引用文献 (4)

8. 文件与曲线 (10)

Files (7)

Curves (3)