Research workbench
Rhodobacter sphaeroides mitochondrial respiratory chain complex
Analyse Rhodobacter sphaeroides mitochondrial respiratory chain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NHG
- Type
- protein
- Length
- 2,080 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130, P07552
- Ligands
- CDL, 6PE, HEM, AZO, 8PE, HEC, FES, MC3
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 446 | 46% helix, 19% strand | P31800 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 425 | 45% helix, 19% strand | P23004 |
| C | Cytochrome B | protein | 378 | 72% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 39% helix, 8% strand | P00125 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 29% helix, 17% strand | P13272 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 105 | 70% helix, 1% strand | P00129 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 75 | 52% helix, 11% strand | P13271 |
| H | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 67 | 75% helix, 0% strand | P00126 |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 34 | 12% helix, 21% strand | P13272 |
| J | Cytochrome B-C1 complex subunit 9 | protein | 61 | 72% helix, 0% strand | P00130 |
| K | Cytochrome B-C1 complex subunit 10 | protein | 52 | 63% helix, 0% strand | P07552 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 3 copies · chains A, C, K, D, F, G
- 6PE · 1,2-dihexanoyl-sn-glycero-3-phosphoethanolamine · ligand · 2 copies · chains A, C, K
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains C
- AZO · Methyl (2Z)-2-(2-{[6-(2-cyanophenoxy)pyrimidin-4-yl]oxy}phenyl)-3-methoxyacrylate · ligand · chains C
- 8PE · (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate · ligand · chains C, F, G
- HEC · Heme C · ligand · chains D
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
- MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · chains A, C, D, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.81 | 0.85 | 76 | HEM |
| 2 | 775 | 0.81 | 0.84 | 70 | 8PE |
| 3 | 702 | 0.81 | 0.85 | 63 | empty |
| 4 | 955 | 0.80 | 0.82 | 72 | empty |
| 5 | 847 | 0.79 | 0.82 | 90 | empty |
Interfaces
20 interfaces between chains.
- A–B · 2311 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1724 Ų buried · 21 hydrogen bonds · protein-protein
- B–I · 1445 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 1284 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 1219 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 cofactor (disulfide, heme c attachment).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P31800
- Every structure of UniProt P23004
- Every structure of UniProt P00157
- Every structure of UniProt P00125
- Every structure of UniProt P13272
- Every structure of UniProt P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Every structure of UniProt P07552
- Elsewhere: RCSB PDB 6NHG · PDBe 6NHG · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552
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