SAXSdb — 1po1

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1po1
沉积日期 deposition_date	1997-01-08
结构标题 title	POLIOVIRUS (TYPE 1, MAHONEY) IN COMPLEX WITH R80633, AN INHIBITOR OF VIRAL REPLICATION
关键词 keywords	POLIOVIRUS, PICORNAVIRUS COAT PROTEIN, ANTI-VIRAL DRUGS, HYDROLASE, THIOL PROTEASE, 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	30.16 Å
回转半径 Rg (电子) rg_electron	29.13 Å
零角强度 I(0) i0	144165000.00
分子量 molecular_weight	95043.0 kDa
排除体积 excluded_volume	118830 Å³
包络体积 envelope_volume	148580 Å³
水化壳体积 shell_volume	41389 Å³
包络直径 envelope_diameter	102.4 Å
壳层 Rg shell_rg	37.11 Å
包络 Rg envelope_rg	29.80 Å
形状 Rg shape_rg	29.11 Å
总 Rg total_rg	29.91 Å
总原子数 total_atoms	6690
残基数 n_residues	853
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	98.0 Å
Rg (实空间) rg_real	30.08 Å
Rg 误差 (实空间) rg_real_error	0.62 Å
I(0) (实空间) i0_real	1.4420e+08
I(0) 误差 (实空间) i0_real_error	2.0720e+06
Rg (倒空间) rg_reciprocal	30.11 Å
I(0) (倒空间) i0_reciprocal	144200000.0000
解质量估计 total_estimate	0.6915
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.0 Å
偏度 Skewness skewness	0.298
峰度 Kurtosis kurtosis	-0.320
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26890000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.999; Smooth: 0.958

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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	POLIOVIRUS TYPE 1 MAHONEY
分子量 formula_weight	437.4 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	0
原子数 atom_count	6690

GSSST

Entity 2 polymer

描述 description	POLIOVIRUS TYPE 1 MAHONEY
分子量 formula_weight	33488.6 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	1

GLGQMLESMIDNTVRETVGAATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDTVQTRHVVQHRSRSESSIESFFARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYVPPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY

Entity 3 polymer

描述 description	POLIOVIRUS TYPE 1 MAHONEY
分子量 formula_weight	30075.8 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

SPNIEACGYSDRVLQLTLGNSTITTQEAANSVVAYGRWPEYLRDSEANPVDQPTEPDVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITLTIAPMCCEFNGLRNITLPRLQ

Entity 4 polymer

描述 description	POLIOVIRUS TYPE 1 MAHONEY
分子量 formula_weight	26547.5 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

GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKALAQ

Entity 5 polymer

描述 description	POLIOVIRUS TYPE 1 MAHONEY
分子量 formula_weight	7393.1 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

GAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLN

Entity 6 non-polymer

描述 description	(METHYLPYRIDAZINE PIPERIDINE BUTYLOXYPHENYL)ETHYLACETATE
分子量 formula_weight	397.5 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

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6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1po1.1
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	d1po11_
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	d1po13_
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 (4 domains)

结构域编号 domain_id	1po1100
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	1po1200
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	1po1300
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	1po1400
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	80 — Rhinovirus 14, subunit 4
同源超家族 H-superfamily homologous superfamily	10 — Picornavirus coat protein VP4

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7. 引用文献 (8)

Ligand-induced conformational changes in poliovirus-antiviral drug complexes.

Acta Crystallogr.,Sect.D (1997)

PMID: 15299887 · DOI: 10.1107/S0907444997000954 PRIMARY

;Binding of the Antiviral Drug Win51711 to the Sabin Strain of Type 3 Poliovirus: Structural Comparison with Drug Binding in Rhinovirus 14 ;

Acta Crystallogr.,Sect.D (1995)

Structures of Poliovirus Complexes with Anti-Viral Drugs: Implications for Viral Stability and Drug Design

Curr.Biol. (1994)

Role of Conformational Transitions in Poliovirus Assembly and Cell Entry

New Aspects of Positive-Strand RNA Viruses (1990)

Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus

Embo J. (1989)

Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance

Nature (1987)

Three-Dimensional Structure of Poliovirus at 2.9 A Resolution

Science (1985)

The Nucleotide Sequence of Poliovirus Type 3 Leon 12 A1B: Comparison with Poliovirus Type 1

Nucleic Acids Res. (1983)

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晶胞边长 a length_a	322.940 Å
晶胞边长 b length_b	358.040 Å
晶胞边长 c length_c	380.150 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 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	— Å
R 因子 r_factor	—
R_work r_work	0.2410
R_free r_free	—

fit	/app/data/saxs_computation/po/1po1/1po1.fit
pddf	/app/data/pr_computation/po/1po1/1po1.pr.out
profile	/app/data/saxs_computation/po/1po1/1po1.dat

POLIOVIRUS (TYPE 1, MAHONEY) IN COMPLEX WITH R80633, AN INHIBITOR OF VIRAL REPLICATION

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. 折叠分类 (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. 引用文献 (8)

8. 文件与曲线 (10)

Files (7)

Curves (3)