Research workbench
Bovine mitochondrial F1-ATPase crystallised in the presence of 5MM amppnp
Analyse Bovine mitochondrial F1-ATPase crystallised in the presence of 5MM amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H8H
- Type
- protein
- Length
- 2,979 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bovine mitochondrial F1-ATPase
- EC
- 3.6.1.34
- UniProt
- P19483, P00829, P05631
- Ligands
- ATP, ADP, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bovine mitochondrial F1-ATPase (EC 3.6.1.34) | protein | 487 | 43% helix, 20% strand | P19483 |
| B | Bovine mitochondrial F1-ATPase (EC 3.6.1.34) | protein | 479 | 43% helix, 21% strand | P19483 |
| C | Bovine mitochondrial F1-ATPase (EC 3.6.1.34) | protein | 492 | 41% helix, 20% strand | P19483 |
| D | Bovine mitochondrial F1-ATPase (EC 3.6.1.34) | protein | 467 | 39% helix, 20% strand | P00829 |
| E, F | Bovine mitochondrial F1-ATPase (EC 3.6.1.34) | protein | 466 | 38% helix, 20% strand | P00829 |
| G | Bovine mitochondrial F1-ATPase (EC 3.6.1.34) | protein | 122 | 89% helix, 0% strand | P05631 |
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 E
- GOL · Glycerol · additive · chains B
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 | 1067 | 0.88 | 0.90 | 119 | GOL |
| 2 | 525 | 0.87 | 0.93 | 87 | ATP, MG |
| 3 | 619 | 0.84 | 0.89 | 57 | ATP, MG |
| 4 | 687 | 0.83 | 0.87 | 102 | empty |
| 5 | 587 | 0.83 | 0.88 | 83 | ADP, MG |
Interfaces
13 interfaces between chains.
- C–D · 3079 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 2637 Ų buried · 33 hydrogen bonds · protein-protein
- C–F · 2332 Ų buried · 23 hydrogen bonds · protein-protein
- B–F · 2217 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 1980 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1H8H · Bovine mitochondrial F1-ATPase crystallised in the presence of 5mm AMPPNP · 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 0.99
- 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 0.95
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 1H8H · PDBe 1H8H · UniProt P19483 · UniProt P00829 · UniProt P05631
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