Research workbench
Monomer yeast ATP synthase fo reconstituted in nanodisc with inhibitor of oligomycin bound generated from focused refinement.
Analyse Monomer yeast ATP synthase fo reconstituted in nanodisc with inhibitor of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CP5
- Type
- protein
- Length
- 1,234 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit 9, mitochondrial; ATP synthase protein 8; ATP synthase subunit a…
- UniProt
- P61829, P00856, P00854, P05626, P30902, Q06405, P81450
- Ligands
- EFO
- Pockets
- 11 · best druggability 0.80
Structure
electron microscopy · 8 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, L, N, O, P, Q, S, T | ATP synthase subunit 9, mitochondrial | protein | 74 | 86% helix, 0% strand | P61829 |
| M, R | ATP synthase subunit 9, mitochondrial | protein | 75 | 85% helix, 0% strand | P61829 |
| 8 | ATP synthase protein 8 | protein | 42 | 93% helix, 0% strand | P00856 |
| X | ATP synthase subunit a | protein | 224 | 78% helix, 0% strand | P00854 |
| Z | ATP synthase subunit 4, mitochondrial | protein | 54 | 93% helix, 0% strand | P05626 |
| 7 | ATP synthase subunit D, mitochondrial | protein | 67 | 55% helix, 1% strand | P30902 |
| U | ATP synthase subunit F, mitochondrial | protein | 68 | 57% helix, 0% strand | Q06405 |
| J | ATP synthase subunit J, mitochondrial | protein | 37 | 54% helix, 0% strand | P81450 |
Ligands and binding sites
- EFO · Oligomycin A · ligand · 4 copies · chains M, N, O, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.80 | 0.81 | 71 | empty |
| 2 | 90 | 0.74 | 0.96 | 21 | empty |
| 3 | 1142 | 0.74 | 0.76 | 64 | empty |
| 4 | 114 | 0.70 | 0.91 | 15 | empty |
| 5 | 261 | 0.64 | 0.80 | 41 | empty |
Interfaces
29 interfaces between chains.
- O–P · 1588 Ų buried · 7 hydrogen bonds · protein-protein
- L–M · 1546 Ų buried · 3 hydrogen bonds · protein-protein
- K–L · 1534 Ų buried · 5 hydrogen bonds · protein-protein
- R–S · 1532 Ų buried · 4 hydrogen bonds · protein-protein
- Q–R · 1513 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 modified (formylation).
Compared structures
- 6CP5 · Monomer yeast ATP synthase Fo reconstituted in nanodisc with inhibitor of oligomycin… · the same entry in another collection · chain T against T, 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 P61829
- Every structure of UniProt P00856
- Every structure of UniProt P00854
- Every structure of UniProt P05626
- Every structure of UniProt P30902
- Every structure of UniProt Q06405
- Every structure of UniProt P81450
- Elsewhere: RCSB PDB 6CP5 · PDBe 6CP5 · UniProt P61829 · UniProt P00856 · UniProt P00854 · UniProt P05626 · UniProt P30902 · UniProt Q06405 · UniProt P81450
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