1ntk
Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1
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
| 条目编号 entry_id | 1ntk |
| 沉积日期 deposition_date | 2003-01-30 |
| 结构标题 title | Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1 |
| 关键词 keywords | MEMBRANE PROTEIN, OXIDOREDUCTASE; OXIDOREDUCTASE |
| 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 | 49.65 Å |
| 回转半径 Rg (电子) rg_electron | 49.44 Å |
| 零角强度 I(0) i0 | 798733000.00 |
| 分子量 molecular_weight | 238100.0 kDa |
| 排除体积 excluded_volume | 299360 ų |
| 包络体积 envelope_volume | 427440 ų |
| 水化壳体积 shell_volume | 73733 ų |
| 包络直径 envelope_diameter | 165.6 Å |
| 壳层 Rg shell_rg | 50.99 Å |
| 包络 Rg envelope_rg | 49.03 Å |
| 形状 Rg shape_rg | 49.44 Å |
| 总 Rg total_rg | 49.52 Å |
| 总原子数 total_atoms | 16776 |
| 残基数 n_residues | 2114 |
| 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/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| 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 | 165.8 Å |
| Rg (实空间) rg_real | 50.00 Å |
| Rg 误差 (实空间) rg_real_error | 1.75 Å |
| I(0) (实空间) i0_real | 7.9870e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.6440e+07 |
| Rg (倒空间) rg_reciprocal | 49.66 Å |
| I(0) (倒空间) i0_reciprocal | 798400000.0000 |
| 解质量估计 total_estimate | 0.8446 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 46.6 Å |
| 偏度 Skewness skewness | 0.410 |
| 峰度 Kurtosis kurtosis | -0.587 |
| 角度范围 angular_range | — – 0.1600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 86500000.0000 |
| 实空间数据点数 n_real_points | 33 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.932; Smooth: 0.518 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (15)
6. 折叠分类 (SCOP + CATH) 31 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1ntka1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.185 — LuxS/MPP-like metallohydrolase |
| 超家族 Superfamily superfamily | d.185.1 — LuxS/MPP-like metallohydrolase |
| 家族 Family family | d.185.1.1 — MPP-like |
| 结构域编号 domain_id | d1ntka2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.185 — LuxS/MPP-like metallohydrolase |
| 超家族 Superfamily superfamily | d.185.1 — LuxS/MPP-like metallohydrolase |
| 家族 Family family | d.185.1.1 — MPP-like |
| 结构域编号 domain_id | d1ntkb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.185 — LuxS/MPP-like metallohydrolase |
| 超家族 Superfamily superfamily | d.185.1 — LuxS/MPP-like metallohydrolase |
| 家族 Family family | d.185.1.1 — MPP-like |
| 结构域编号 domain_id | d1ntkb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.185 — LuxS/MPP-like metallohydrolase |
| 超家族 Superfamily superfamily | d.185.1 — LuxS/MPP-like metallohydrolase |
| 家族 Family family | d.185.1.1 — MPP-like |
| 结构域编号 domain_id | d1ntkc1 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 超家族 Superfamily superfamily | f.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d1ntkc2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.1 — Transmembrane di-heme cytochromes |
| 家族 Family family | f.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d1ntkd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.3 — Cytochrome c |
| 超家族 Superfamily superfamily | a.3.1 — Cytochrome c |
| 家族 Family family | a.3.1.3 — Cytochrome bc1 domain |
| 结构域编号 domain_id | d1ntkd2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.11 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor |
| 家族 Family family | f.23.11.1 — Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor |
| 结构域编号 domain_id | d1ntke1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.33 — ISP domain |
| 超家族 Superfamily superfamily | b.33.1 — ISP domain |
| 家族 Family family | b.33.1.1 — Rieske iron-sulfur protein (ISP) |
| 结构域编号 domain_id | d1ntke2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.12 — ISP transmembrane anchor |
| 家族 Family family | f.23.12.1 — ISP transmembrane anchor |
| 结构域编号 domain_id | d1ntkf_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.27 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 超家族 Superfamily superfamily | f.27.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.27.1.1 — 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d1ntkg_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.13 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.23.13.1 — Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d1ntkh_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.28 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 超家族 Superfamily superfamily | f.28.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.28.1.1 — Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d1ntki_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.184 — Non-globular alpha+beta subunits of globular proteins |
| 超家族 Superfamily superfamily | d.184.1 — Non-globular alpha+beta subunits of globular proteins |
| 家族 Family family | d.184.1.3 — Ubiquinol-cytochrome c reductase 8 kDa protein |
| 结构域编号 domain_id | d1ntkj_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.14 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.23.14.1 — Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d1ntkk_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.15 — Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.23.15.1 — Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
CATH v4.4 (15 domains)
| 结构域编号 domain_id | 1ntkA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 830 — Cytochrome Bc1 Complex; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Metalloenzyme, LuxS/M16 peptidase-like |
| 结构域编号 domain_id | 1ntkA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 830 — Cytochrome Bc1 Complex; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Metalloenzyme, LuxS/M16 peptidase-like |
| 结构域编号 domain_id | 1ntkB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 830 — Cytochrome Bc1 Complex; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Metalloenzyme, LuxS/M16 peptidase-like |
| 结构域编号 domain_id | 1ntkB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 830 — Cytochrome Bc1 Complex; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Metalloenzyme, LuxS/M16 peptidase-like |
| 结构域编号 domain_id | 1ntkC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 810 — Cytochrome Bc1 Complex; Chain C |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome Bc1 Complex; Chain C |
| 结构域编号 domain_id | 1ntkD01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 100 — Cytochrome c1, transmembrane anchor, C-terminal |
| 结构域编号 domain_id | 1ntkD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 760 — Cytochrome Bc1 Complex; Chain D, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome c-like domain |
| 结构域编号 domain_id | 1ntkE01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 270 — Ubiquinol cytochrome reductase, transmembrane domain |
| 结构域编号 domain_id | 1ntkE02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 102 — 3-layer Sandwich |
| 拓扑 Topology topology | 10 — Rieske Iron-sulfur Protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — Rieske [2Fe-2S] iron-sulphur domain |
| 结构域编号 domain_id | 1ntkF00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1090 — Cytochrome Bc1 Complex; Chain F |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome b-c1 complex subunit 7 |
| 结构域编号 domain_id | 1ntkG00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 210 — Cytochrome b-c1 complex subunit 8 |
| 结构域编号 domain_id | 1ntkH00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ubiquinol-cytochrome C reductase hinge domain |
| 结构域编号 domain_id | 1ntkI00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 210 — Cytochrome Bc1 Complex; Chain I |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome Bc1 Complex; Chain I |
| 结构域编号 domain_id | 1ntkJ00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 260 — Cytochrome b-c1 complex subunit 9 |
| 结构域编号 domain_id | 1ntkK00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 220 — |