1g9m

HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

Method: X-RAY DIFFRACTION D_max: 134.7 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	1g9m
沉积日期 deposition_date	2000-11-24
结构标题 title	HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B
关键词 keywords	;COMPLEX (HIV ENVELOPE PROTEIN-CD4-FAB), HIV-1 EXTERIOR ENVELOPE GP120 FROM LABORATORY-ADAPTED ISOLATE, HXBC2, SURFACE T-CELL GLYCOPROTEIN CD4, ANTIGEN-BINDING FRAGMENT OF HUMAN IMMUNOGLOBULIN 17B, Viral protein-Immune system COMPLEX ;; Viral protein/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	39.28 Å
回转半径 Rg (电子) rg_electron	39.45 Å
零角强度 I(0) i0	172212000.00
分子量 molecular_weight	104930.0 kDa
排除体积 excluded_volume	130900 Å³
包络体积 envelope_volume	180950 Å³
水化壳体积 shell_volume	40789 Å³
包络直径 envelope_diameter	139.5 Å
壳层 Rg shell_rg	41.95 Å
包络 Rg envelope_rg	39.22 Å
形状 Rg shape_rg	39.42 Å
总 Rg total_rg	39.69 Å
总原子数 total_atoms	7369
残基数 n_residues	929
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	134.7 Å
Rg (实空间) rg_real	39.59 Å
Rg 误差 (实空间) rg_real_error	1.75 Å
I(0) (实空间) i0_real	1.7220e+08
I(0) 误差 (实空间) i0_real_error	3.2720e+06
Rg (倒空间) rg_reciprocal	39.41 Å
I(0) (倒空间) i0_reciprocal	172200000.0000
解质量估计 total_estimate	0.8511
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	131.3 Å
偏度 Skewness skewness	0.400
峰度 Kurtosis kurtosis	-0.584
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16140000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.855

▶

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

▶

5. 实体与聚合体信息 (8)

Entity 1 polymer

描述 description	ENVELOPE GLYCOPROTEIN GP120
分子量 formula_weight	35429.1 kDa
突变 mutation	VARIABLE LOOPS SUBSTITUTED
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	G
原子数 atom_count	8322

GARSEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTGAGHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIE

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI 分类编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Drosophila melanogaster

Entity 2 polymer

描述 description	T-CELL SURFACE GLYCOPROTEIN CD4
分子量 formula_weight	20503.3 kDa
突变 mutation	S184N, I185T
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	C

KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQKASNT

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	Cricetulus griseus

Entity 3 polymer

描述 description	ANTIBODY 17B, LIGHT CHAIN
分子量 formula_weight	23440.0 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	L

ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQKSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

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	Mus musculus

Entity 4 polymer

描述 description	ANTIBODY 17B, HEAVY CHAIN
分子量 formula_weight	24525.6 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	H

QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYRNNGFLKHWGQGTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPQPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

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	Mus musculus

Entity 5 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	2

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	12

Entity 7 non-polymer

描述 description	ISOPROPYL ALCOHOL
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	953

▼

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

结构域编号 domain_id	d1g9mc1
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	d1g9mc2
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.1.1.3 — C2 set domains

结构域编号 domain_id	d1g9mg_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.172 — gp120 core
超家族 Superfamily superfamily	d.172.1 — gp120 core
家族 Family family	d.172.1.1 — gp120 core

结构域编号 domain_id	d1g9mh1
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	d1g9mh2
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	d1g9ml1
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	d1g9ml2
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 (7 domains)

结构域编号 domain_id	1g9mC01
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	1g9mC02
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	1g9mG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	170 — Beta Complex
拓扑 Topology topology	40 — HIV Envelope Protein Gp120; Chain G
同源超家族 H-superfamily homologous superfamily	20 — Human immunodeficiency virus 1, Gp160, envelope glycoprotein

结构域编号 domain_id	1g9mH01
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	1g9mH02
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	1g9mL01
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	1g9mL02
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 (2)

▶

晶胞边长 a length_a	71.250 Å
晶胞边长 b length_b	88.110 Å
晶胞边长 c length_c	196.540 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 2 2 21
空间群编号 int_tables_number	17
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2676
R_free r_free	0.3299

fit	/app/data/saxs_computation/g9/1g9m/1g9m.fit
pddf	/app/data/pr_computation/g9/1g9m/1g9m.pr.out
profile	/app/data/saxs_computation/g9/1g9m/1g9m.dat

HIV-1 HXBC2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B

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 (8)

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

来源 Source

Entity 4 polymer

聚合体 Polymer

来源 Source

Entity 5 branched

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)