MolNFT v1 · #5365 · protein
Bovine mitochondrial F1-ATPase complexed with the peptide antibiotic efrapeptin
1EFR · Bovine mitochondrial F1-ATPase subunit alpha: “Bovine mitochondrial F1-ATPase complexed with the peptide antibiotic efrapeptin”. X-ray diffraction, 5 ligands (ANP, ACE, TLX), 20 pockets (best druggability 0.87). MolNFT v1 #5365 on…
- PDB
- 1EFR
- Type
- protein
- Length
- 3,002 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bovine mitochondrial F1-ATPase subunit alpha; Bovine mitochondrial F1-ATPase subunit…
- EC
- 3.6.1.34
- UniProt
- P19483, P00829, P05631
- Ligands
- ANP, ACE, TLX, ADP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bovine mitochondrial F1-ATPase subunit alpha (EC 3.6.1.34) | protein | 487 | 43% helix, 20% strand | P19483 |
| C | Bovine mitochondrial F1-ATPase subunit alpha (EC 3.6.1.34) | protein | 492 | 41% helix, 20% strand | P19483 |
| D | Bovine mitochondrial F1-ATPase subunit beta (EC 3.6.1.34) | protein | 467 | 39% helix, 21% strand | P00829 |
| E, F | Bovine mitochondrial F1-ATPase subunit beta (EC 3.6.1.34) | protein | 466 | 37% helix, 19% strand | P00829 |
| G | Bovine mitochondrial F1-ATPase subunit gamma (EC 3.6.1.34) | protein | 122 | 88% helix, 0% strand | P05631 |
| Q | Efrapeptin C | protein | 15 | 40% helix, 0% strand | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains A, D, B, E, C, F
- ACE · Acetyl group · ligand · chains G, Q
- TLX · N1-(2-amino-4-methylpentyl)octahydro-pyrrolo[1,2-A] pyrimidine · ligand · chains B, E, Q
- ADP · Adenosine-5'-diphosphate · ligand · chains C, D
- 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 | 724 | 0.87 | 0.91 | 92 | MG, ANP |
| 2 | 879 | 0.84 | 0.86 | 90 | TLX, MG, ANP |
| 3 | 555 | 0.84 | 0.89 | 73 | empty |
| 4 | 712 | 0.84 | 0.87 | 72 | empty |
| 5 | 729 | 0.84 | 0.87 | 97 | empty |
Interfaces
17 interfaces between chains.
- C–D · 2978 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2551 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 2303 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 2214 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 1907 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 1EFR · Bovine mitochondrial F1-ATPase complexed with the peptide antibiotic efrapeptin · the same entry in another collection · chain Q against Q, 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
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 1EFR · PDBe 1EFR · UniProt P19483 · UniProt P00829 · UniProt P05631
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