MolNFT v1 · #114462 · protein
Structure of the yeast F1FO ATPase C10 ring with oligomycin B
5BQ6 · ATP synthase subunit 9, mitochondrial: “Structure of the yeast F1FO ATPase C10 ring with oligomycin B”. X-ray diffraction, 1 ligand (EFB), 4 pockets (best druggability 0.65). MolNFT v1 #114462 on GenesisL1: 3D structure, binding…
- PDB
- 5BQ6
- Type
- protein
- Length
- 746 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit 9, mitochondrial
- EC
- 3.6.-.-
- UniProt
- P61829
- Ligands
- EFB
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | ATP synthase subunit 9, mitochondrial (EC 3.6.-.-) | protein | 74 | 91% helix, 0% strand | P61829 |
| B, C, K, L, M, N | ATP synthase subunit 9, mitochondrial (EC 3.6.-.-) | protein | 75 | 89% helix, 0% strand | P61829 |
| O | ATP synthase subunit 9, mitochondrial (EC 3.6.-.-) | protein | 74 | 91% helix, 0% strand | P61829 |
Ligands and binding sites
- EFB · oligomycin B · ligand · 7 copies · chains A, B, C, M, D, E, K, L, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.65 | 0.76 | 44 | empty |
| 2 | 268 | 0.52 | 0.74 | 37 | empty |
| 3 | 104 | 0.33 | 0.72 | 21 | empty |
| 4 | 83 | 0.29 | 0.72 | 20 | empty |
Interfaces
11 interfaces between chains.
- M–N · 1558 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1554 Ų buried · 3 hydrogen bonds · protein-protein
- K–L · 1546 Ų buried · 5 hydrogen bonds · protein-protein
- L–M · 1539 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1527 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (formylation).
Compared structures
- 5BQ6 · Structure of the yeast F1FO ATPase C10 ring with oligomycin B · the same entry in another collection · chain O against O, TM-score 1.00
- P61829 · AlphaFold monomer V2.0 prediction for ATP synthase subunit 9, mitochondrial (P61829) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P61829
- Elsewhere: RCSB PDB 5BQ6 · PDBe 5BQ6 · UniProt P61829
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