MolNFT v1 · #144442 · protein
Structure of alternative complex III from flavobacterium johnsoniae (wild type)
6BTM · Alternative complex III subunit a: “Structure of alternative complex III from flavobacterium johnsoniae (wild type)”. Electron microscopy, 4 ligands (HEC, E87, F3S), 20 pockets (best druggability 0.89). MolNFT v1 #144442 on…
- PDB
- 6BTM
- Type
- protein
- Length
- 2,361 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alternative complex III subunit a; Alternative complex III subunit B; Alternative complex…
- UniProt
- A5FJF1, A5FJF2, A5FJF3, A5FJF4, A5FJF5, A5FJE2
- Ligands
- HEC, E87, F3S, SF4
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 6 distinct chains · 43% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alternative complex III subunit a | protein | 221 | 30% helix, 4% strand | A5FJF1 |
| B | Alternative complex III subunit B | protein | 948 | 24% helix, 18% strand | A5FJF2 |
| C | Alternative complex III subunit C | protein | 457 | 68% helix, 0% strand | A5FJF3 |
| D | Alternative complex III subunit D | protein | 172 | 49% helix, 12% strand | A5FJF4 |
| E | Alternative complex III subunit E | protein | 161 | 27% helix, 1% strand | A5FJF5 |
| F | Alternative complex III subunit F | protein | 402 | 73% helix, 0% strand | A5FJE2 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, E, B, C, D
- E87 · (2R)-3-{[(2R)-2-(decanoylamino)-3-hydroxypropyl]sulfanyl}propane-1,2-diyl ditetradecanoate · ligand · 2 copies · chains A, B, C, E
- F3S · FE3-S4 cluster · ligand · chains B
- SF4 · Iron/sulfur 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.89 | 0.91 | 137 | empty |
| 2 | 899 | 0.89 | 0.92 | 94 | empty |
| 3 | 548 | 0.87 | 0.92 | 78 | HEC |
| 4 | 263 | 0.83 | 0.94 | 45 | empty |
| 5 | 1108 | 0.79 | 0.81 | 115 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2778 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2562 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2226 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 21 hydrogen bonds · protein-protein
- C–F · 1738 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 2 covalent, 2 disulfide (heme c attachment, covalent ligand, disulfide).
Compared structures
- 6BTM · Structure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type) · the same entry in another collection · chain B against B, 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 A5FJF1
- Every structure of UniProt A5FJF2
- Every structure of UniProt A5FJF3
- Every structure of UniProt A5FJF4
- Every structure of UniProt A5FJF5
- Every structure of UniProt A5FJE2
- Elsewhere: RCSB PDB 6BTM · PDBe 6BTM · UniProt A5FJF1 · UniProt A5FJF2 · UniProt A5FJF3 · UniProt A5FJF4 · UniProt A5FJF5 · UniProt A5FJE2
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