Research workbench
Monomer yeast ATP synthase (F1FO) reconstituted in nanodisc with inhibitor of oligomycin bound.
Analyse Monomer yeast ATP synthase (F1FO) 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
- 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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