SAXSdb — 2hwd

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hwd
沉积日期 deposition_date	1994-01-25
结构标题 title	A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A
关键词 keywords	RHINOVIRUS COAT PROTEIN, Icosahedral virus, Virus; VIRUS
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	29.44 Å
回转半径 Rg (电子) rg_electron	28.61 Å
零角强度 I(0) i0	127898000.00
分子量 molecular_weight	88815.0 kDa
排除体积 excluded_volume	110800 Å³
包络体积 envelope_volume	137010 Å³
水化壳体积 shell_volume	39115 Å³
包络直径 envelope_diameter	100.7 Å
壳层 Rg shell_rg	36.44 Å
包络 Rg envelope_rg	29.16 Å
形状 Rg shape_rg	28.61 Å
总 Rg total_rg	29.35 Å
总原子数 total_atoms	6246
残基数 n_residues	793
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	94.1 Å
Rg (实空间) rg_real	29.39 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	1.2790e+08
I(0) 误差 (实空间) i0_real_error	1.8590e+06
Rg (倒空间) rg_reciprocal	29.41 Å
I(0) (倒空间) i0_reciprocal	127900000.0000
解质量估计 total_estimate	0.8923
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	34.9 Å
偏度 Skewness skewness	0.314
峰度 Kurtosis kurtosis	-0.300
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	31450000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.901

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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 (5)

Entity 1 polymer

描述 description	HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1)
分子量 formula_weight	32610.7 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	1
原子数 atom_count	6246

NPVENYIDEVLNEVLVVPNIKESHHTTSNSAPLLDAAETGHTSNVQPEDAIETRYVITSQTRDEMSIESFLGRSGCVHISRIKVDYTDYNGQDINFTKWKITLQEMAQIRRKFELFTYVRFDSEITLVPCIAGRGDDIGHIVMQYMYVPPGAPIPSKRNDFSWQSGTNMSIFWQHGQPFPRFSIPFLSIASAYYMFYDGYDGDNTSSKYGSVVTNDMGTICSRIVTEKQKLSVVITTHIYHKAKHTKAWCPRPPRAVPYTHSHVTNYMPETGDVTTAIVRRNTITTA

来源 Source

来源生物 organism	Human rhinovirus 1A
NCBI 分类编号 ncbi_taxonomy_id	12134
宿主生物 host_organism	Homo sapiens

Entity 2 polymer

描述 description	HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2)
分子量 formula_weight	29114.8 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	2

SPSVEACGYSDRIMQITRGDSTISSDDVANAVVGYGVWPHYLTPQDATAINKPTQPDTSSNRFYTLESKHWNGSSKGWWWKLPDALKDMGIFGENMYYHFLGRSGYTVHVQCNASKFHQGTLLVAMIPEHQLASAKHGSVTAGYKLTHPGEAGRDVSQERDASLRQPSDDSWLNFDGTLLGNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWCLVIIPISPLRSETTSSNIVPITVSISPMCAEFSGARAKNIKQ

来源 Source

来源生物 organism	Human rhinovirus 1A
NCBI 分类编号 ncbi_taxonomy_id	12134
宿主生物 host_organism	Homo sapiens

Entity 3 polymer

描述 description	HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3)
分子量 formula_weight	26177.0 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	3

GLPVYITPGSGQFMTTDDMQSPCALPWYHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGNNVGNVSMYTVQLGNQTGMAQKVFSIKVDITSTPLATTLIGEIASYYTHWTGSLRFSFMFCGTANTTLKLLLAYTPPGIDEPTTRKDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTADNKYSMAGYITCWYQTNLVVPPSTPQTADMLCFVSACKDFCLRMARDTDLHIQSGPIEQ

来源 Source

来源生物 organism	Human rhinovirus 1A
NCBI 分类编号 ncbi_taxonomy_id	12134
宿主生物 host_organism	Homo sapiens

Entity 4 polymer

描述 description	HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4)
分子量 formula_weight	4583.8 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	4

GAGVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLD

来源 Source

来源生物 organism	Human rhinovirus 1A
NCBI 分类编号 ncbi_taxonomy_id	12134
宿主生物 host_organism	Homo sapiens

Entity 5 non-polymer

描述 description	5-(3-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PROPYL)-3-METHYL ISOXAZOLE
分子量 formula_weight	355.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d2hwd.1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

结构域编号 domain_id	d2hwd1_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

结构域编号 domain_id	d2hwd3_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
超家族 Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
家族 Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (3 domains)

结构域编号 domain_id	2hwd100
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2hwd200
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	2hwd300
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	20 —

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7. 引用文献 (6)

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晶胞边长 a length_a	341.300 Å
晶胞边长 b length_b	341.300 Å
晶胞边长 c length_c	465.900 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	120.00 °
晶胞分子数 Z z_pdb	120

空间群 space_group	P 63 2 2
空间群编号 int_tables_number	182
晶系 crystal_system	—

分辨率 resolution	3.800 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/hw/2hwd/2hwd.fit
pddf	/app/data/pr_computation/hw/2hwd/2hwd.pr.out
profile	/app/data/saxs_computation/hw/2hwd/2hwd.dat

A COMPARISON OF THE ANTI-RHINOVIRAL DRUG BINDING POCKET IN HRV14 AND HRV1A

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

5. 实体与聚合体信息 (5)

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 non-polymer

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (6)

8. 文件与曲线 (10)

Files (7)

Curves (3)