MolNFT v1 · #188256 · protein
Yeast ATP synthase F1 region state 1-3BINDING BETA_TIGHT open without exogenous ATP
7TJU · ATP synthase subunit alpha: “Yeast ATP synthase F1 region state 1-3BINDING BETA_TIGHT open without exogenous ATP”. Electron microscopy, 3 ligands (ATP, MG, PO4), 20 pockets (best druggability 0.87). MolNFT v1 #188256 on GenesisL1…
- PDB
- 7TJU
- Type
- protein
- Length
- 3,102 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, MG, PO4
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha | protein | 482 | 43% helix, 21% strand | P07251 |
| B | ATP synthase subunit alpha | protein | 478 | 43% helix, 22% strand | P07251 |
| C | ATP synthase subunit alpha | protein | 482 | 43% helix, 21% strand | P07251 |
| D, E, F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 40% helix, 21% strand | P00830 |
| G | ATP synthase subunit gamma | protein | 256 | 70% helix, 11% strand | P38077 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains 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 | 890 | 0.87 | 0.89 | 103 | ATP, MG |
| 2 | 1062 | 0.86 | 0.87 | 111 | ATP, MG |
| 3 | 999 | 0.83 | 0.84 | 87 | ATP, MG |
| 4 | 705 | 0.81 | 0.85 | 91 | empty |
| 5 | 469 | 0.81 | 0.88 | 63 | empty |
Interfaces
12 interfaces between chains.
- B–F · 2787 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 2409 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2036 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 1939 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 1924 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7TJU · Yeast ATP synthase F1 region State 1-3binding beta_tight open without exogenous 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 E against A, TM-score 0.96
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 7TJU · PDBe 7TJU · UniProt P07251 · UniProt P00830 · UniProt P38077
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