MolNFT v1 · #111803 · protein
Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphate.
4Z1M · ATP synthase subunit alpha, mitochondrial: “Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of…”. X-ray diffraction, 4 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.88).…
- PDB
- 4Z1M
- Type
- protein
- Length
- 3,143 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
- EC
- 3.6.3.14
- UniProt
- P19483, P00829, P05631, P01096
- Ligands
- ATP, ADP, MG, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 9 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, mitochondrial | protein | 487 | 41% helix, 19% strand | P19483 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 487 | 39% helix, 20% strand | P19483 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 483 | 39% helix, 19% strand | P19483 |
| D, F | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 469 | 38% helix, 19% strand | P00829 |
| E | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) | protein | 470 | 36% helix, 19% strand | P00829 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 187 | 70% helix, 3% strand | P05631 |
| H | ATPase inhibitor, mitochondrial | protein | 41 | 83% helix, 0% strand | P01096 |
| I | ATPase inhibitor, mitochondrial | protein | 28 | 89% helix, 0% strand | P01096 |
| J | ATPase inhibitor, mitochondrial | protein | 22 | 77% helix, 0% strand | P01096 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, D, B, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CL · Chloride ion · ion · 11 copies · chains B, C, E, F, G, D
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 1103 | 0.88 | 0.90 | 126 | ATP, MG, CL |
| 2 | 770 | 0.88 | 0.91 | 99 | ATP, MG |
| 3 | 778 | 0.85 | 0.88 | 76 | ATP, MG |
| 4 | 628 | 0.84 | 0.88 | 67 | empty |
| 5 | 978 | 0.82 | 0.83 | 129 | GOL |
Interfaces
22 interfaces between chains.
- A–D · 2558 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2503 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 2240 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2122 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 2115 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4Z1M · Bovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in… · the same entry in another collection · chain J against J, 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
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 P01096
- Elsewhere: RCSB PDB 4Z1M · PDBe 4Z1M · UniProt P19483 · UniProt P00829 · UniProt P05631 · UniProt P01096
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