MolNFT v1 · #145470 · protein
Monomer yeast ATP synthase (F1FO) reconstituted in nanodisc with inhibitor of oligomycin bound.
6CP3 · ATP synthase subunit 9, mitochondrial: “Monomer yeast ATP synthase (F1FO) reconstituted in nanodisc with inhibitor of oligomycin bound.”. Electron microscopy, 2 ligands (ATP, ADP), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6CP3
- Type
- protein
- Length
- 5,128 residues
- Chains
- 27
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit 9, mitochondrial; ATP synthase subunit 5, mitochondrial; ATP…
- EC
- 7.1.2.2
- UniProt
- P61829, P09457, P07251, P00830, P38077, Q12165, P21306, P05626, P30902, Q12349, Q06405, P00856, P00854, P81450
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 19 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, L, N, O, P, Q, S, T | ATP synthase subunit 9, mitochondrial | protein | 74 | 89% helix, 0% strand | P61829 |
| M, R | ATP synthase subunit 9, mitochondrial | protein | 75 | 85% helix, 0% strand | P61829 |
| Y | ATP synthase subunit 5, mitochondrial | protein | 187 | 45% helix, 7% strand | P09457 |
| A | ATP synthase subunit alpha, mitochondrial | protein | 507 | 40% helix, 18% strand | P07251 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 506 | 40% helix, 18% strand | P07251 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 508 | 39% helix, 18% strand | P07251 |
| D | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 470 | 35% helix, 20% strand | P00830 |
| E | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 473 | 35% helix, 18% strand | P00830 |
| F | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 472 | 37% helix, 19% strand | P00830 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 269 | 61% helix, 12% strand | P38077 |
| H | ATP synthase subunit delta, mitochondrial | protein | 132 | 27% helix, 37% strand | Q12165 |
| I | ATP synthase subunit epsilon, mitochondrial | protein | 59 | 34% helix, 8% strand | P21306 |
| Z | ATP synthase subunit 4, mitochondrial | protein | 155 | 90% helix, 0% strand | P05626 |
| 7 | ATP synthase subunit D, mitochondrial | protein | 171 | 61% helix, 1% strand | P30902 |
| 6 | ATP synthase subunit H, mitochondrial | protein | 89 | 42% helix, 0% strand | Q12349 |
| U | ATP synthase subunit F, mitochondrial | protein | 85 | 46% helix, 0% strand | Q06405 |
| 8 | ATP synthase protein 8 | protein | 42 | 90% helix, 0% strand | P00856 |
| X | ATP synthase subunit a | protein | 224 | 74% helix, 0% strand | P00854 |
| J | ATP synthase subunit J, mitochondrial | protein | 37 | 54% helix, 0% strand | P81450 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D, B, F
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 | 1043 | 0.85 | 0.86 | 94 | empty |
| 2 | 1140 | 0.84 | 0.85 | 122 | ADP |
| 3 | 568 | 0.84 | 0.90 | 81 | ADP |
| 4 | 751 | 0.83 | 0.87 | 59 | ATP |
| 5 | 970 | 0.83 | 0.84 | 88 | ATP |
Interfaces
72 interfaces between chains.
- C–D · 2811 Ų buried · 32 hydrogen bonds · protein-protein
- Z–7 · 2679 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2674 Ų buried · 37 hydrogen bonds · protein-protein
- B–F · 2525 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 2505 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (formylation).
Compared structures
- 6CP3 · Monomer yeast ATP synthase (F1Fo) reconstituted in nanodisc with inhibitor of oligomycin… · the same entry in another collection · chain N against N, 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 P09457
- Every structure of UniProt P07251
- Every structure of UniProt P00830
- Every structure of UniProt P38077
- Every structure of UniProt Q12165
- Every structure of UniProt P21306
- Every structure of UniProt P05626
- Every structure of UniProt P30902
- Every structure of UniProt Q12349
- Every structure of UniProt Q06405
- Every structure of UniProt P00856
- Every structure of UniProt P00854
- Every structure of UniProt P81450
- Elsewhere: RCSB PDB 6CP3 · PDBe 6CP3 · UniProt P61829 · UniProt P09457 · UniProt P07251 · UniProt P00830 · UniProt P38077 · UniProt Q12165 · UniProt P21306 · UniProt P05626 · UniProt P30902 · UniProt Q12349 · UniProt Q06405 · UniProt P00856 · UniProt P00854 · UniProt P81450
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