MolNFT v1 · #25612 · protein
Beryllium fluoride inhibited bovine F1-ATPase
1W0J · ATP synthase alpha chain heart isoform, mitochondrial…: “Beryllium fluoride inhibited bovine F1-ATPase”. X-ray diffraction, 4 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.88). MolNFT v1 #25612 on GenesisL1: 3D structure…
- PDB
- 1W0J
- Type
- protein
- Length
- 3,056 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase alpha chain heart isoform, mitochondrial precursor; ATP synthase beta chain…
- EC
- 3.6.3.14
- UniProt
- P19483, P00829, P05631
- Ligands
- ADP, BEF, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase alpha chain heart isoform, mitochondrial precursor (EC 3.6.3.14) | protein | 487 | 42% helix, 20% strand | P19483 |
| B | ATP synthase alpha chain heart isoform, mitochondrial precursor (EC 3.6.3.14) | protein | 480 | 41% helix, 20% strand | P19483 |
| C | ATP synthase alpha chain heart isoform, mitochondrial precursor (EC 3.6.3.14) | protein | 498 | 41% helix, 20% strand | P19483 |
| D | ATP synthase beta chain, mitochondrial precursor (EC 3.6.3.14) | protein | 467 | 39% helix, 20% strand | P00829 |
| E, F | ATP synthase beta chain, mitochondrial precursor (EC 3.6.3.14) | protein | 466 | 36% helix, 21% strand | P00829 |
| G | ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14) | protein | 192 | 67% helix, 7% strand | P05631 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, D, B, E, C, F
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains C, D, B, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · chains E
- GOL · Glycerol · additive · 4 copies · chains A, B, 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 | 1044 | 0.88 | 0.89 | 105 | ADP, MG |
| 2 | 754 | 0.87 | 0.91 | 100 | ADP, MG |
| 3 | 818 | 0.83 | 0.86 | 67 | ADP, MG |
| 4 | 751 | 0.83 | 0.86 | 78 | empty |
| 5 | 1148 | 0.83 | 0.83 | 109 | ADP, MG, BEF |
Interfaces
13 interfaces between chains.
- C–D · 3078 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2582 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2395 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 2327 Ų buried · 35 hydrogen bonds · protein-protein
- B–E · 2053 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1W0J · Beryllium fluoride inhibited bovine F1-ATPase · the same entry in another collection · chain G against G, TM-score 1.00
- P19483 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P19483) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P00829 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, mitochondrial (P00829) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P05631 · AlphaFold monomer V2.0 prediction for ATP synthase subunit gamma, mitochondrial (P05631) · a predicted model of the same protein · chain G 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 P19483
- Every structure of UniProt P00829
- Every structure of UniProt P05631
- Elsewhere: RCSB PDB 1W0J · PDBe 1W0J · UniProt P19483 · UniProt P00829 · UniProt P05631
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.