SAXSdb — 1qjy

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1qjy
沉积日期 deposition_date	1999-07-06
结构标题 title	HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099
关键词 keywords	;VIRUS, NUCLEOTIDYLTRANSFERASE, RHINOVIRUS COAT PROTEIN, RNA-BINDING, TRANSFERASE, LIPOPROTEIN, WIN COMPOUND, PHOSPHOPROTEIN, THIOL PROTEASE, CAPSID PROTEIN, DRUG, VIRION, MEMBRANE, HELICASE, PROTEASE, NUCLEOTIDE-BINDING, HUMAN RHINOVIRUS 16, RNA REPLICATION, ANTIVIRAL COMPOUND, COVALENT PROTEIN-RNA LINKAGE, MYRISTATE, HYDROLASE, CYTOPLASM, ATP-BINDING, CYTOPLASMIC VESICLE, HOST-VIRUS INTERACTION, RNA-DIRECTED RNA POLYMERASE ;; 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	29.59 Å
回转半径 Rg (电子) rg_electron	28.73 Å
零角强度 I(0) i0	131780000.00
分子量 molecular_weight	90588.0 kDa
排除体积 excluded_volume	113140 Å³
包络体积 envelope_volume	139780 Å³
水化壳体积 shell_volume	39602 Å³
包络直径 envelope_diameter	101.2 Å
壳层 Rg shell_rg	36.67 Å
包络 Rg envelope_rg	29.32 Å
形状 Rg shape_rg	28.70 Å
总 Rg total_rg	29.53 Å
总原子数 total_atoms	6376
残基数 n_residues	804
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	93.3 Å
Rg (实空间) rg_real	29.51 Å
Rg 误差 (实空间) rg_real_error	0.57 Å
I(0) (实空间) i0_real	1.3180e+08
I(0) 误差 (实空间) i0_real_error	2.0460e+06
Rg (倒空间) rg_reciprocal	29.55 Å
I(0) (倒空间) i0_reciprocal	131800000.0000
解质量估计 total_estimate	0.8964
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	36.3 Å
偏度 Skewness skewness	0.289
峰度 Kurtosis kurtosis	-0.337
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	27260000.0000
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: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.900

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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 (8)

Entity 1 polymer

描述 description	PROTEIN VP1
分子量 formula_weight	32501.4 kDa
来源方法 src_method	nat
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	6679

NPVERYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Entity 2 polymer

描述 description	PROTEIN VP2
分子量 formula_weight	28990.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	2

SPSVEACGYSDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSSNRFYTLDSKMWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQGTLLVVMIPEHQLATVNKGNVNAGYKYTHPGEAGREVGTQVENEKQPSDDNWLNFDGTLLGNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPITVSISPMCAEFSGARAKTVVQ

Entity 3 polymer

描述 description	PROTEIN VP3
分子量 formula_weight	26314.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	3

GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQSNIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFCGTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTPDTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Entity 4 polymer

描述 description	PROTEIN VP4
分子量 formula_weight	7374.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	4

GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVLEKGIPTLQ

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 6 non-polymer

描述 description	2,6-DIMETHYL-1-(3-[3-METHYL-5-ISOXAZOLYL]-PROPANYL)-4-[2-METHYL-4-ISOXAZOLYL]-PHENOL
分子量 formula_weight	326.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 non-polymer

描述 description	MYRISTIC ACID
分子量 formula_weight	228.4 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	303

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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	d1qjy.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	d1qjy1_
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	d1qjy3_
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	1qjy100
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	1qjy200
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	1qjy300
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 (7)

Analysis of Three Structurally Related Antiviral Compounds in Complex with Human Rhinovirus 16

Proc.Natl.Acad.Sci.USA (1999)

PMID: 10611281 · DOI: 10.1073/PNAS.96.26.14730 PRIMARY

The Refined Structure of Human Rhinovirus 16 at 2.15 Angstroms Resolution: Implications for the Viral Life Cycle

Structure (1997)

PMID: 9083115 · DOI: 10.1016/S0969-2126(97)00199-8

The Structure of Human Rhinovirus 16

Structure (1993)

PMID: 7915182 · DOI: 10.1016/0969-2126(93)90008-5

A Comparison of the Anti-Rhinoviral Drug Binding Pocket in Hrv14 and Hrv1A

J.Mol.Biol. (1993)

PMID: 8383771 · DOI: 10.1006/JMBI.1993.1137

Crystal Structure of Human Rhinovirus Serotype 1A (Hrv1A)

J.Mol.Biol. (1989)

PMID: 2555523 · DOI: 10.1016/0022-2836(89)90293-3

The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating

Science (1986)

PMID: 3018924 · DOI: 10.1126/SCIENCE.3018924

Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses

Nature (1985)

PMID: 2993920 · DOI: 10.1038/317145A0

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晶胞边长 a length_a	362.600 Å
晶胞边长 b length_b	347.100 Å
晶胞边长 c length_c	334.900 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	90.00 °
晶胞分子数 Z z_pdb	120

空间群 space_group	P 2 21 21
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.800 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2330

fit	/app/data/saxs_computation/qj/1qjy/1qjy.fit
pddf	/app/data/pr_computation/qj/1qjy/1qjy.pr.out
profile	/app/data/saxs_computation/qj/1qjy/1qjy.dat

HUMAN RHINOVIRUS 16 COAT PROTEIN IN COMPLEX WITH ANTIVIRAL COMPOUND VP65099

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (7)

8. 文件与曲线 (10)

Files (7)

Curves (3)