2hai

Crystal structure of HCV NS5B RNA polymerase in complex with novel class of dihydropyrone-containing inhibitor.

Method: X-RAY DIFFRACTION D_max: 74.4 Å Quality: EXCELLENT

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	2hai
沉积日期 deposition_date	2006-06-12
结构标题 title	Crystal structure of HCV NS5B RNA polymerase in complex with novel class of dihydropyrone-containing inhibitor.
关键词 keywords	HCV RNA Polymerase, Transferase; TRANSFERASE
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	25.01 Å
回转半径 Rg (电子) rg_electron	23.97 Å
零角强度 I(0) i0	63678800.00
分子量 molecular_weight	61720.0 kDa
排除体积 excluded_volume	77054 Å³
包络体积 envelope_volume	91156 Å³
水化壳体积 shell_volume	31021 Å³
包络直径 envelope_diameter	76.3 Å
壳层 Rg shell_rg	31.68 Å
包络 Rg envelope_rg	23.81 Å
形状 Rg shape_rg	23.97 Å
总 Rg total_rg	24.82 Å
总原子数 total_atoms	4330
残基数 n_residues	560
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	74.4 Å
Rg (实空间) rg_real	24.87 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	6.3680e+07
I(0) 误差 (实空间) i0_real_error	7.5540e+05
Rg (倒空间) rg_reciprocal	24.91 Å
I(0) (倒空间) i0_reciprocal	63680000.0000
解质量估计 total_estimate	0.9141
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	31.9 Å
偏度 Skewness skewness	0.108
峰度 Kurtosis kurtosis	-0.569
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11250000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.990

▶

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

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	HEPATITIS C VIRUS NS5B RNA POLYMERASE
分子量 formula_weight	64270.6 kDa
EC 编号 ec_number	2.7.7.48
突变 mutation	K114R, L47Q, F101Y
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	4929

SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKYGYGAKDVRNLSSRAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHSLSRARPRHHHHHH

来源 Source

来源生物 organism	Hepatitis C virus
NCBI 分类编号 ncbi_taxonomy_id	11103
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	(6S)-6-CYCLOPENTYL-6-[2-(3-FLUORO-4-ISOPROPOXYPHENYL)ETHYL]-4-HYDROXY-5,6-DIHYDRO-2H-PYRAN-2-ONE
分子量 formula_weight	362.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	596

▼

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2haia_
类 Class class	e — Multi-domain proteins (alpha and beta)
折叠类型 Fold fold	e.8 — DNA/RNA polymerases
超家族 Superfamily superfamily	e.8.1 — DNA/RNA polymerases
家族 Family family	e.8.1.4 — RNA-dependent RNA-polymerase

CATH v4.4 (1 domains)

结构域编号 domain_id	2haiA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	83.255 Å
晶胞边长 b length_b	83.255 Å
晶胞边长 c length_c	179.830 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	8

空间群 space_group	P 41 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	1.580 Å
最低分辨率 resolution_low	22.000 Å
R 因子 r_factor	0.2154
R_work r_work	0.2150
R_free r_free	0.2363

fit	/app/data/saxs_computation/ha/2hai/2hai.fit
pddf	/app/data/pr_computation/ha/2hai/2hai.pr.out
profile	/app/data/saxs_computation/ha/2hai/2hai.dat