Research workbench
Yeast ATP synthase F1 region state 1CATALYTIC(E-H) with 10 mm ATP
Analyse Yeast ATP synthase F1 region state 1CATALYTIC(E-H) 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
- 7TJW
- Type
- protein
- Length
- 3,097 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
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha | protein | 478 | 42% helix, 21% strand | P07251 |
| B | ATP synthase subunit alpha | protein | 475 | 43% helix, 21% strand | P07251 |
| C | ATP synthase subunit alpha | protein | 483 | 42% helix, 22% strand | P07251 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 465 | 39% helix, 22% strand | P00830 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 468 | 38% helix, 18% strand | P00830 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 469 | 41% helix, 21% strand | P00830 |
| G | ATP synthase subunit gamma | protein | 259 | 68% helix, 8% strand | P38077 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, D, B, C, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, 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 | 1002 | 0.87 | 0.88 | 105 | ATP, MG |
| 2 | 980 | 0.86 | 0.87 | 112 | ATP, MG |
| 3 | 825 | 0.85 | 0.88 | 88 | ATP, MG |
| 4 | 799 | 0.83 | 0.85 | 73 | ATP |
| 5 | 1188 | 0.82 | 0.83 | 99 | ATP, MG |
Interfaces
12 interfaces between chains.
- C–D · 2529 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 2333 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2316 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2131 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1830 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 7TJW · Yeast ATP synthase F1 region State 1catalytic(e-h) 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
- P38077 · AlphaFold monomer V2.0 prediction for ATP synthase subunit gamma, mitochondrial (P38077) · a predicted model of the same protein · chain G against A, TM-score 0.97
- 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 0.97
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 7TJW · PDBe 7TJW · UniProt P07251 · UniProt P00830 · UniProt P38077
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.