Research workbench
Rat liver F1-ATPase
Analyse Rat liver F1-ATPase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F43
- Type
- protein
- Length
- 1,075 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase alpha chain, mitochondrial; ATP synthase beta chain, mitochondrial; ATP…
- EC
- 3.6.3.14
- UniProt
- P15999, P10719, P35435
- Ligands
- ATP, ADP, MG, VO4
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase alpha chain, mitochondrial (EC 3.6.3.14) | protein | 480 | 31% helix, 18% strand | P15999 |
| B | ATP synthase beta chain, mitochondrial (EC 3.6.3.14) | protein | 471 | 29% helix, 18% strand | P10719 |
| G | ATP synthase gamma chain, mitochondrial (EC 3.6.3.14) | protein | 124 | 69% helix, 0% strand | P35435 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.87 | 0.88 | 122 | MG, ATP |
| 2 | 740 | 0.81 | 0.85 | 83 | empty |
| 3 | 883 | 0.73 | 0.77 | 68 | empty |
| 4 | 77 | 0.68 | 0.93 | 23 | empty |
| 5 | 103 | 0.65 | 0.89 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2338 Ų buried · 25 hydrogen bonds · protein-protein
- B–G · 210 Ų buried · 0 hydrogen bonds · protein-protein
- A–G · 173 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2F43 · Rat liver F1-ATPase · the same entry in another collection · chain A against A, TM-score 1.00
- P15999 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P15999) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P10719 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, mitochondrial (P10719) · a predicted model of the same protein · chain B against A, TM-score 0.86
- P35435 · AlphaFold monomer V2.0 prediction for ATP synthase subunit gamma, mitochondrial (P35435) · a predicted model of the same protein · chain G against A, TM-score 0.82
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 P15999
- Every structure of UniProt P10719
- Every structure of UniProt P35435
- Elsewhere: RCSB PDB 2F43 · PDBe 2F43 · UniProt P15999 · UniProt P10719 · UniProt P35435
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