MolNFT v1 · #148227 · protein
Alternative complex III
6F0K · Cytochrome C family protein: “Alternative complex III”. Electron microscopy, 3 ligands (HEC, SF4, F3S), 20 pockets (best druggability 0.89). MolNFT v1 #148227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6F0K
- Type
- protein
- Length
- 2,504 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C family protein; Fe-S-cluster-containing hydrogenase; Polysulphide reductase…
- UniProt
- D0MDD4, D0MDD5, D0MDD6, D0MDD7, D0MDD8, D0MDD9, D0MKF0
- Ligands
- HEC, SF4, F3S
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 7 distinct chains · 43% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C family protein | protein | 207 | 34% helix, 0% strand | D0MDD4 |
| B | Fe-S-cluster-containing hydrogenase | protein | 961 | 23% helix, 9% strand | D0MDD5 |
| C | Polysulphide reductase nrfd | protein | 445 | 68% helix, 0% strand | D0MDD6 |
| D | Actd | protein | 171 | 39% helix, 4% strand | D0MDD7 |
| E | QUINOL:CYTOCHROME C oxidoreductase monoheme cytochrome subunit | protein | 182 | 32% helix, 1% strand | D0MDD8 |
| F | Actf | protein | 382 | 68% helix, 0% strand | D0MDD9 |
| H | Acth | protein | 156 | 63% helix, 0% strand | D0MKF0 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, B, C, D, E
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B
- F3S · FE3-S4 cluster · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1175 | 0.89 | 0.90 | 139 | HEC |
| 2 | 915 | 0.89 | 0.90 | 113 | empty |
| 3 | 342 | 0.86 | 0.96 | 52 | empty |
| 4 | 539 | 0.86 | 0.92 | 63 | HEC |
| 5 | 95 | 0.76 | 0.97 | 23 | empty |
Interfaces
17 interfaces between chains.
- C–D · 2821 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2604 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 2418 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1944 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1860 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 cofactor, 3 covalent (heme c attachment, covalent ligand).
Compared structures
- 6F0K · Alternative complex III · the same entry in another collection · chain A against A, TM-score 1.00
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 D0MDD4
- Every structure of UniProt D0MDD5
- Every structure of UniProt D0MDD6
- Every structure of UniProt D0MDD7
- Every structure of UniProt D0MDD8
- Every structure of UniProt D0MDD9
- Every structure of UniProt D0MKF0
- Elsewhere: RCSB PDB 6F0K · PDBe 6F0K · UniProt D0MDD4 · UniProt D0MDD5 · UniProt D0MDD6 · UniProt D0MDD7 · UniProt D0MDD8 · UniProt D0MDD9 · UniProt D0MKF0
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