2brl

Crystal structure of Hepatitis C virus polymerase in complex with an allosteric inhibitor (compound 2)

Method: X-RAY DIFFRACTION D_max: 74.9 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	2brl
沉积日期 deposition_date	2005-05-06
结构标题 title	Crystal structure of Hepatitis C virus polymerase in complex with an allosteric inhibitor (compound 2)
关键词 keywords	TRANSFERASE, HEPATITIS C VIRUS, HCV, NS5B, POLYMERASE, RNA-DEPENDENT RNA- POLYMERASE, ALLOSTERIC INHIBITOR, NUCLEOTIDYLTRANSFERASE; 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	25.18 Å
回转半径 Rg (电子) rg_electron	24.20 Å
零角强度 I(0) i0	55066700.00
分子量 molecular_weight	57253.0 kDa
排除体积 excluded_volume	71577 Å³
包络体积 envelope_volume	87572 Å³
水化壳体积 shell_volume	29796 Å³
包络直径 envelope_diameter	77.2 Å
壳层 Rg shell_rg	31.64 Å
包络 Rg envelope_rg	23.89 Å
形状 Rg shape_rg	24.21 Å
总 Rg total_rg	25.01 Å
总原子数 total_atoms	4007
残基数 n_residues	512
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	74.9 Å
Rg (实空间) rg_real	25.05 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	5.5070e+07
I(0) 误差 (实空间) i0_real_error	6.6940e+05
Rg (倒空间) rg_reciprocal	25.09 Å
I(0) (倒空间) i0_reciprocal	55070000.0000
解质量估计 total_estimate	0.9168
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	73.8 Å
偏度 Skewness skewness	0.112
峰度 Kurtosis kurtosis	-0.593
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	8865000.0000
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: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.993

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	RNA-DIRECTED RNA POLYMERASE
分子量 formula_weight	59641.5 kDa
EC 编号 ec_number	2.7.7.48
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	4366

SMSYTWTGALITPCAAEESKLPINALSNSLLRHHNMVYATTSRSAGLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDVRNLSSKAVNHIHSVWKDLLEDTVTPIDTTIMAKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQVVMGSSYGFQYSPGQRVEFLVNTWKSKKNPMGFSYDTRCFDSTVTENDIRVEESIYQCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAASLRVFTEAMTRYSAPPGDPPQPEYDLELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVKTKLKL

来源 Source

来源生物 organism	HEPATITIS C VIRUS
通用名 common_name	HCV
NCBI 分类编号 ncbi_taxonomy_id	11103
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	MANGANESE (II) ION
分子量 formula_weight	54.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	3-CYCLOHEXYL-1-(2-{METHYL[(1-METHYLPIPERIDIN-3-YL)METHYL]AMINO}-2-OXOETHYL)-2-PHENYL-1H-INDOLE-6-CARBOXYLIC ACID
分子量 formula_weight	501.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 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	354

▼

6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2brla_
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	2brlA03
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	68.303 Å
晶胞边长 b length_b	94.854 Å
晶胞边长 c length_c	96.230 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 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	2.400 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.1930
R_work r_work	0.1890
R_free r_free	0.2550

fit	/app/data/saxs_computation/br/2brl/2brl.fit
pddf	/app/data/pr_computation/br/2brl/2brl.pr.out
profile	/app/data/saxs_computation/br/2brl/2brl.dat