1l5g

CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN AVB3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND

Method: X-RAY DIFFRACTION D_max: 129.4 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1l5g
沉积日期 deposition_date	2002-03-06
结构标题 title	CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN AVB3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND
关键词 keywords	;GENU, HYBRID DOMAIN, BETA-TAIL DOMAIN, PSI DOMAIN, EGF DOMAIN, MIDAS, ADMIDAS, LIMBS, CAGE MOTIF, PROPELLER, A-DOMAIN, THIGH DOMAIN, CALF DOMAIN, RGD LIGAND, CELL ADHESION ;; CELL ADHESION
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	40.10 Å
回转半径 Rg (电子) rg_electron	39.66 Å
零角强度 I(0) i0	439968000.00
分子量 molecular_weight	167190.0 kDa
排除体积 excluded_volume	207540 Å³
包络体积 envelope_volume	286920 Å³
水化壳体积 shell_volume	60507 Å³
包络直径 envelope_diameter	138.6 Å
壳层 Rg shell_rg	45.32 Å
包络 Rg envelope_rg	38.80 Å
形状 Rg shape_rg	39.65 Å
总 Rg total_rg	40.01 Å
总原子数 total_atoms	11700
残基数 n_residues	1470
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	129.4 Å
Rg (实空间) rg_real	39.99 Å
Rg 误差 (实空间) rg_real_error	1.34 Å
I(0) (实空间) i0_real	4.4000e+08
I(0) 误差 (实空间) i0_real_error	8.2950e+06
Rg (倒空间) rg_reciprocal	40.10 Å
I(0) (倒空间) i0_reciprocal	440000000.0000
解质量估计 total_estimate	0.8970
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	53.1 Å
偏度 Skewness skewness	0.183
峰度 Kurtosis kurtosis	-0.474
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	51050000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.919

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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	INTEGRIN ALPHA V
分子量 formula_weight	105880.2 kDa
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	11700

FNLDVDSPAEYSGPEGSYFGFAVDFFVPSASSRMFLLVGAPKANTTQPGIVEGGQVLKCDWSSTRRCQPIEFDATGNRDYAKDDPLEFKSHQWFGASVRSKQDKILACAPLYHWRTEMKQEREPVGTCFLQDGTKTVEYAPCRSQDIDADGQGFCQGGFSIDFTKADRVLLGGPGSFYWQGQLISDQVAEIVSKYDPNVYSIKYNNQLATRTAQAIFDDSYLGYSVAVGDFNGDGIDDFVSGVPRAARTLGMVYIYDGKNMSSLYNFTGEQMAAYFGFSVAATDINGDDYADVFIGAPLFMDRGSDGKLQEVGQVSVSLQRASGDFQTTKLNGFEVFARFGSAIAPLGDLDQDGFNDIAIAAPYGGEDKKGIVYIFNGRSTGLNAVPSQILEGQWAARSMPPSFGYSMKGATDIDKNGYPDLIVGAFGVDRAILYRARPVITVNAGLEVYPSILNQDNKTCSLPGTALKVSCFNVRFCLKADGKGVLPRKLNFQVELLLDKLKQKGAIRRALFLYSRSPSHSKNMTISRGGLMQCEELIAYLRDESEFRDKLTPITIFMEYRLDYRTAADTTGLQPILNQFTPANISRQAHILLDCGEDNVCKPKLEVSVDSDQKKIYIGDDNPLTLIVKAQNQGEGAYEAELIVSIPLQADFIGVVRNNEALARLSCAFKTENQTRQVVCDLGNPMKAGTQLLAGLRFSVHQQSEMDTSVKFDLQIQSSNLFDKVSPVVSHKVDLAVLAAVEIRGVSSPDHVFLPIPNWEHKENPETEEDVGPVVQHIYELRNNGPSSFSKAMLHLQWPYKYNNNTLLYILHYDIDGPMNCTSDMEINPLRIKISSLQTTEKNDTVAGQGERDHLITKRDLALSEGDIHTLGCGVAQCLKIVCQVGRLDRGKSAILYVKSLLWTETFMNKENQNHSYSLKSSASFNVIEFPYKNLPIEDITNSTLVTTNVTWGIQP

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	Spodoptera frugiperda

Entity 2 polymer

描述 description	INTEGRIN BETA-3
分子量 formula_weight	76650.3 kDa
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	B

GPNICTTRGVSSCQQCLAVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEFPVSEARVLEDRPLSDKGSGDSSQVTQVSPQRIALRLRPDDSKNFSIQVRQVEDYPVDIYYLMDLSYSMKDDLWSIQNLGTKLATQMRKLTSNLRIGFGAFVDKPVSPYMYISPPEALENPCYDMKTTCLPMFGYKHVLTLTDQVTRFNEEVKKQSVSRNRDAPEGGFDAIMQATVCDEKIGWRNDASHLLVFTTDAKTHIALDGRLAGIVQPNDGQCHVGSDNHYSASTTMDYPSLGLMTEKLSQKNINLIFAVTENVVNLYQNYSELIPGTTVGVLSMDSSNVLQLIVDAYGKIRSKVELEVRDLPEELSLSFNATCLNNEVIPGLKSCMGLKIGDTVSFSIEAKVRGCPQEKEKSFTIKPVGFKDSLIVQVTFDCDCACQAQAEPNSHRCNNGNGTFECGVCRCGPGWLGSQCECSEEDYRPSQQDECSPREGQPVCSQRGECLCGQCVCHSSDFGKITGKYCECDDFSCVRYKGEMCSGHGQCSCGDCLCDSDWTGYYCNCTTRTDTCMSSNGLLCSGRGKCECGSCVCIQPGSYGDTCEKCPTCPDACTFKKECVECKKFDREPYMTENTCNRYCRDEIESVKELKDTGKDAVNCTYKNEDDCVVRFQYYEDSSGKSILYVVEEPECPKGPD

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	Spodoptera frugiperda

Entity 3 polymer

描述 description	CYCLIC ARG-GLY-ASP PEPTIDE
分子量 formula_weight	607.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

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

RGDFV

Entity 4 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	4

Entity 5 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	3

Entity 6 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	4

Entity 7 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

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6. 折叠分类 (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

结构域编号 domain_id	d1l5ga1
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.1.15 — Integrin domains
家族 Family family	b.1.15.1 — Integrin domains

结构域编号 domain_id	d1l5ga2
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.1.15 — Integrin domains
家族 Family family	b.1.15.1 — Integrin domains

结构域编号 domain_id	d1l5ga3
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.1.15 — Integrin domains
家族 Family family	b.1.15.1 — Integrin domains

结构域编号 domain_id	d1l5ga4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.8 — Integrin alpha N-terminal domain
家族 Family family	b.69.8.1 — Integrin alpha N-terminal domain

结构域编号 domain_id	d1l5gb1
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.1.15 — Integrin domains
家族 Family family	b.1.15.1 — Integrin domains

结构域编号 domain_id	d1l5gb2
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	d1l5gb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.200 — Integrin beta tail domain
超家族 Superfamily superfamily	d.200.1 — Integrin beta tail domain
家族 Family family	d.200.1.1 — Integrin beta tail domain

结构域编号 domain_id	d1l5gb4
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.6 — Integrin beta EGF-like domains

结构域编号 domain_id	d1l5gb5
类 Class class	g — Small proteins
折叠类型 Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
超家族 Superfamily superfamily	g.3.11 — EGF/Laminin
家族 Family family	g.3.11.6 — Integrin beta EGF-like domains

CATH v4.4 (8 domains)

结构域编号 domain_id	1l5gA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	130 — Integrin alpha, N-terminal

结构域编号 domain_id	1l5gA02
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	1460 — Integrin domains. Chain A, domain 2

结构域编号 domain_id	1l5gA03
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	1510 — ntegrin, alpha v. Chain A, domain 3

结构域编号 domain_id	1l5gA04
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	1530 — ntegrin, alpha v. Chain A, domain 4

结构域编号 domain_id	1l5gB01
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	1510 — ntegrin, alpha v. Chain A, domain 3

结构域编号 domain_id	1l5gB02
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	1l5gB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	10 — Ribbon
拓扑 Topology topology	25 — Laminin
同源超家族 H-superfamily homologous superfamily	10 — Laminin

结构域编号 domain_id	1l5gB04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1240 — Hormone receptor fold
同源超家族 H-superfamily homologous superfamily	30 —

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7. 引用文献 (1)

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晶胞边长 a length_a	129.790 Å
晶胞边长 b length_b	129.790 Å
晶胞边长 c length_c	308.780 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	120.00 °
晶胞分子数 Z z_pdb	6

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	3.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2480
R_free r_free	0.3280

fit	/app/data/saxs_computation/l5/1l5g/1l5g.fit
pddf	/app/data/pr_computation/l5/1l5g/1l5g.pr.out
profile	/app/data/saxs_computation/l5/1l5g/1l5g.dat

CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN AVB3 IN COMPLEX WITH AN ARG-GLY-ASP LIGAND

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

来源 Source

Entity 3 polymer

聚合体 Polymer

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 17 domains

SCOP 2.08 (9 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)