Research workbench
Structure of thermophilic F1-ATPase inhibited by epsilon subunit
Analyse Structure of thermophilic F1-ATPase inhibited by epsilon subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XD7
- Type
- protein
- Length
- 3,161 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
- EC
- 3.6.3.14
- UniProt
- Q5KUJ1, Q5KUJ3, Q5KUJ2, Q5KUJ4
- Ligands
- ADP, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 477 | 38% helix, 18% strand | Q5KUJ1 |
| B | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 423 | 32% helix, 18% strand | Q5KUJ1 |
| C | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 475 | 35% helix, 18% strand | Q5KUJ1 |
| D | ATP synthase subunit beta (EC 3.6.3.14) | protein | 470 | 37% helix, 20% strand | Q5KUJ3 |
| E | ATP synthase subunit beta (EC 3.6.3.14) | protein | 469 | 34% helix, 18% strand | Q5KUJ3 |
| F | ATP synthase subunit beta (EC 3.6.3.14) | protein | 464 | 34% helix, 21% strand | Q5KUJ3 |
| G | ATP synthase gamma chain | protein | 254 | 54% helix, 6% strand | Q5KUJ2 |
| H | ATP synthase epsilon chain | protein | 129 | 21% helix, 33% strand | Q5KUJ4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains B, F
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, 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 | 765 | 0.86 | 0.89 | 87 | SO4 |
| 2 | 630 | 0.84 | 0.89 | 85 | empty |
| 3 | 518 | 0.84 | 0.90 | 58 | empty |
| 4 | 586 | 0.82 | 0.87 | 87 | empty |
| 5 | 1054 | 0.82 | 0.83 | 90 | empty |
Interfaces
17 interfaces between chains.
- C–D · 2216 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 1996 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1994 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 1946 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1895 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 77 modified (engineered).
Compared structures
- 4XD7 · Structure of thermophilic F1-ATPase inhibited by epsilon subunit · the same entry in another collection · chain H against H, TM-score 1.00
- Q5KUJ1 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha (Q5KUJ1) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q5KUJ3 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta (Q5KUJ3) · a predicted model of the same protein · chain D 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 Q5KUJ1
- Every structure of UniProt Q5KUJ3
- Every structure of UniProt Q5KUJ2
- Every structure of UniProt Q5KUJ4
- Elsewhere: RCSB PDB 4XD7 · PDBe 4XD7 · UniProt Q5KUJ1 · UniProt Q5KUJ3 · UniProt Q5KUJ2 · UniProt Q5KUJ4
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