MolNFT v1 · #41102 · protein
Ground state structure of F1-ATPase from bovine heart mitochondria (bovine F1-ATPase crystallised in the absence of azide)
2JDI · ATP synthase subunit alpha heart isoform: “Ground state structure of F1-ATPase from bovine heart mitochondria (bovine F1-ATPase crystallised in the…”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.87).…
- PDB
- 2JDI
- Type
- protein
- Length
- 3,142 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha heart isoform; ATP synthase subunit beta; ATP synthase gamma…
- EC
- 3.6.3.14, 3.6.1.34
- UniProt
- P19483, P00829, P05631, P05630, P05632
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ATP synthase subunit alpha heart isoform (EC 3.6.3.14) | protein | 487 | 42% helix, 19% strand | P19483 |
| B | ATP synthase subunit alpha heart isoform (EC 3.6.3.14) | protein | 480 | 41% helix, 20% strand | P19483 |
| D | ATP synthase subunit beta (EC 3.6.3.14) | protein | 467 | 40% helix, 20% strand | P00829 |
| E | ATP synthase subunit beta (EC 3.6.3.14) | protein | 458 | 36% helix, 22% strand | P00829 |
| F | ATP synthase subunit beta (EC 3.6.3.14) | protein | 466 | 39% helix, 20% strand | P00829 |
| G | ATP synthase gamma chain (EC 3.6.1.34) | protein | 184 | 69% helix, 4% strand | P05631 |
| H | ATP synthase delta chain (EC 3.6.1.34) | protein | 88 | 30% helix, 14% strand | P05630 |
| I | ATP synthase epsilon chain (EC 3.6.1.34) | protein | 25 | 52% helix, 0% strand | P05632 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 5 copies · chains A, D, B, E, 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 | 718 | 0.87 | 0.91 | 89 | ANP, MG |
| 2 | 674 | 0.87 | 0.91 | 98 | ANP, MG |
| 3 | 482 | 0.84 | 0.91 | 59 | ANP, MG |
| 4 | 1025 | 0.83 | 0.84 | 122 | empty |
| 5 | 885 | 0.83 | 0.85 | 91 | ANP, MG |
Interfaces
16 interfaces between chains.
- C–D · 3147 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 2604 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 2405 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 2297 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 2015 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2JDI · Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase… · the same entry in another collection · chain I against I, 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 C 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 0.98
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
- Every structure of UniProt P05630
- Every structure of UniProt P05632
- Elsewhere: RCSB PDB 2JDI · PDBe 2JDI · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P05630 · UniProt P05632
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