6hja

Xray structure of GLIC in complex with glutarate

Method: X-RAY DIFFRACTION Dmax: 124.4 Å Quality: GOOD

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Proton-gated ion channel

Gloeobacter violaceus (strain PCC 7421)

UniProt Q7NDN8

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白同源多聚体 同源多聚体 蛋白 × 5 PDB 声明:pentameric(5) 与蛋白拷贝数一致 链 A; UniProt 1–359 链 B; UniProt 1–359 链 C; UniProt 1–359 链 D; UniProt 1–359 链 E; UniProt 1–359 未记录 PLC DIUNDECYL PHOSPHATIDYL CHOLINE × 14 CL CHLORIDE ION × 11 D12 DODECANE × 6 GUA GLUTARIC ACID × 5 NA SODIUM ION × 4 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;291 K;100 mM Na-Acetate pH4 400 mM Na-Isothiocyanate 12-15% PEG4000 2% DMSO 16% Glycerol 分辨率 2.70 Å R-free 0.219

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 129 个其他 PDB 条目、135 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 GLIC_GLOVI
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–359; UniProt 1–359 作者链 B; PDB构建体 1–359; UniProt 1–359 作者链 C; PDB构建体 1–359; UniProt 1–359 作者链 D; PDB构建体 1–359; UniProt 1–359 作者链 E; PDB构建体 1–359; UniProt 1–359

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 6hja

P(r) 距离分布 P(r) Distribution

P(r) distribution for 6hja
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id6hja
沉积日期 deposition_date2018-09-03
结构标题 titleXray structure of GLIC in complex with glutarate
关键词 keywordsPentameric Ligand-Gated Ion channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier37.99
回转半径 Rg (电子) rg_electron37.18
零角强度 I(0) i0407037000.00
分子量 molecular_weight184820.0 kDa
排除体积 excluded_volume239630 ų
包络体积 envelope_volume297370 ų
水化壳体积 shell_volume65071 ų
包络直径 envelope_diameter128.5
壳层 Rg shell_rg44.78
包络 Rg envelope_rg36.83
形状 Rg shape_rg37.17
总 Rg total_rg37.74
总原子数 total_atoms13083
残基数 n_residues1555
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax124.4
Rg (实空间) rg_real37.89
Rg 误差 (实空间) rg_real_error1.17
I(0) (实空间) i0_real4.0700e+08
I(0) 误差 (实空间) i0_real_error6.9980e+06
Rg (倒空间) rg_reciprocal37.95
I(0) (倒空间) i0_reciprocal407100000.0000
解质量估计 total_estimate0.8760
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary47.4
偏度 Skewness skewness0.315
峰度 Kurtosis kurtosis-0.275
角度范围 angular_range— – 0.2100 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha66440000.0000
实空间数据点数 n_real_points43
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.911

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (7)

7. 折叠分类 (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

结构域编号 domain_id6hjaA01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjaA02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjaB01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjaB02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjaC01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjaC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjaD01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjaD02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain
结构域编号 domain_id6hjaE01
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology170 — Acetylcholine Binding Protein; Chain: A,
同源超家族 H-superfamily homologous superfamily10 — Neurotransmitter-gated ion-channel ligand-binding domain
结构域编号 domain_id6hjaE02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily390 — Neurotransmitter-gated ion-channel transmembrane domain

8. 引用文献 (1)

9. 文件与曲线 (10)