Research workbench
F1-ATPase from mycobacterium smegmatis
Analyse F1-ATPase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FOC
- Type
- protein
- Length
- 3,073 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit ALPHA,ATP synthase subunit ALPHA,ATP synthase subunit alpha; ATP…
- EC
- 3.6.3.14
- UniProt
- A0R202, A0R200, A0R201, A0R1Z9
- Ligands
- ADP, MG, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 8 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit ALPHA,ATP synthase subunit ALPHA,ATP synthase subunit alpha (EC 3.6.3.14) | protein | 481 | 40% helix, 19% strand | A0R202 |
| B | ATP synthase subunit ALPHA,ATP synthase subunit ALPHA,ATP synthase subunit alpha (EC 3.6.3.14) | protein | 464 | 41% helix, 20% strand | A0R202 |
| C | ATP synthase subunit ALPHA,ATP synthase subunit ALPHA,ATP synthase subunit alpha (EC 3.6.3.14) | protein | 469 | 41% helix, 19% strand | A0R202 |
| D | ATP synthase subunit beta (EC 3.6.3.14) | protein | 451 | 38% helix, 21% strand | A0R200 |
| E | ATP synthase subunit beta (EC 3.6.3.14) | protein | 448 | 38% helix, 19% strand | A0R200 |
| F | ATP synthase subunit beta (EC 3.6.3.14) | protein | 454 | 38% helix, 22% strand | A0R200 |
| G | ATP synthase gamma chain | protein | 193 | 79% helix, 2% strand | A0R201 |
| H | ATP synthase epsilon chain | protein | 113 | 15% helix, 50% strand | A0R1Z9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · chains A, E
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 | 990 | 0.89 | 0.90 | 119 | ADP, MG |
| 2 | 863 | 0.87 | 0.89 | 114 | ADP, MG |
| 3 | 442 | 0.83 | 0.91 | 50 | ADP, MG |
| 4 | 358 | 0.83 | 0.92 | 44 | empty |
| 5 | 523 | 0.82 | 0.88 | 73 | ADP, MG |
Interfaces
14 interfaces between chains.
- C–D · 2930 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 2438 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 2384 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 2271 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 2198 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6FOC · F1-ATPase from Mycobacterium smegmatis · the same entry in another collection · chain H against H, TM-score 1.00
- A0R202 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha (A0R202) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A0R200 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta (A0R200) · 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 A0R202
- Every structure of UniProt A0R200
- Every structure of UniProt A0R201
- Every structure of UniProt A0R1Z9
- Elsewhere: RCSB PDB 6FOC · PDBe 6FOC · UniProt A0R202 · UniProt A0R200 · UniProt A0R201 · UniProt A0R1Z9
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