Research workbench
Yeast ATP synthase F1 region state 1BINDING(A-D) with 10 mm ATP
Analyse Yeast ATP synthase F1 region state 1BINDING(A-D) with 10 mm ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TJX
- Type
- protein
- Length
- 3,072 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase subunit gamma
- EC
- 7.1.2.2
- UniProt
- P07251, P00830, P38077
- Ligands
- ATP, ADP, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha | protein | 471 | 45% helix, 22% strand | P07251 |
| B | ATP synthase subunit alpha | protein | 477 | 39% helix, 21% strand | P07251 |
| C | ATP synthase subunit alpha | protein | 484 | 43% helix, 20% strand | P07251 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 453 | 37% helix, 22% strand | P00830 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 456 | 36% helix, 21% strand | P00830 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 467 | 40% helix, 22% strand | P00830 |
| G | ATP synthase subunit gamma | protein | 264 | 63% helix, 9% strand | P38077 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · chains C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · chains C, D
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 | 1111 | 0.88 | 0.89 | 146 | ATP, MG |
| 2 | 895 | 0.86 | 0.88 | 112 | ATP, MG |
| 3 | 730 | 0.85 | 0.88 | 83 | ATP, MG |
| 4 | 595 | 0.83 | 0.88 | 64 | ATP, MG |
| 5 | 810 | 0.81 | 0.83 | 106 | empty |
Interfaces
12 interfaces between chains.
- B–F · 2696 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 2472 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2406 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1922 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1864 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7TJX · Yeast ATP synthase F1 region State 1binding(a-d) with 10 mM ATP · the same entry in another collection · chain G against G, TM-score 1.00
- P07251 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P07251) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P00830 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, mitochondrial (P00830) · 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 P07251
- Every structure of UniProt P00830
- Every structure of UniProt P38077
- Elsewhere: RCSB PDB 7TJX · PDBe 7TJX · UniProt P07251 · UniProt P00830 · UniProt P38077
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