MolNFT v2 · #211744 · protein
Human ATP synthase F1 domain, state 3a
8H9L · ATP synthase subunit alpha, mitochondrial: “Human ATP synthase F1 domain, state 3a”. Electron microscopy at 2.61, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.87). MolNFT v2 #211744 on GenesisL1: 3D structure, binding…
- PDB
- 8H9L
- Type
- protein
- Length
- 3,128 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.61
- Source
- Homo sapiens
- Molecule
- ATP synthase subunit alpha, mitochondrial; ATP synthase subunit beta, mitochondrial; ATP…
- EC
- 7.1.2.2
- UniProt
- P25705, P06576, P36542, Q9UII2, P48047
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 2.61 · 9 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, mitochondrial | protein | 486 | 44% helix, 21% strand | P25705 |
| B | ATP synthase subunit alpha, mitochondrial | protein | 477 | 42% helix, 21% strand | P25705 |
| C | ATP synthase subunit alpha, mitochondrial | protein | 470 | 41% helix, 21% strand | P25705 |
| E | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 456 | 37% helix, 21% strand | P06576 |
| F | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 466 | 40% helix, 21% strand | P06576 |
| D | ATP synthase subunit beta, mitochondrial (EC 7.1.2.2) | protein | 470 | 39% helix, 19% strand | P06576 |
| G | ATP synthase subunit gamma, mitochondrial | protein | 81 | 93% helix, 0% strand | P36542 |
| J | ATPase inhibitor, mitochondrial | protein | 35 | 74% helix, 0% strand | Q9UII2 |
| O | ATP synthase subunit O, mitochondrial | protein | 187 | 60% helix, 12% strand | P48047 |
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 B, F, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, F, D
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 | 710 | 0.87 | 0.91 | 92 | ATP, MG |
| 2 | 1079 | 0.86 | 0.88 | 144 | ADP, MG |
| 3 | 347 | 0.84 | 0.94 | 73 | empty |
| 4 | 1018 | 0.84 | 0.85 | 99 | ATP, MG |
| 5 | 659 | 0.83 | 0.87 | 68 | empty |
Interfaces
22 interfaces between chains.
- A–D · 2459 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2287 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 2234 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2070 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 2014 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- P25705 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, mitochondrial (P25705) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P06576 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, mitochondrial (P06576) · a predicted model of the same protein · chain E against A, TM-score 0.98
- P48047 · AlphaFold monomer V2.0 prediction for ATP synthase subunit O, mitochondrial (P48047) · a predicted model of the same protein · chain O against A, TM-score 0.98
- P36542 · AlphaFold monomer V2.0 prediction for ATP synthase subunit gamma, mitochondrial (P36542) · a predicted model of the same protein · chain G against A, TM-score 0.96
- Q9UII2 · AlphaFold monomer V2.0 prediction for ATPase inhibitor, mitochondrial (Q9UII2) · a predicted model of the same protein · chain J against A, TM-score 0.90
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 P25705
- Every structure of UniProt P06576
- Every structure of UniProt P36542
- Every structure of UniProt Q9UII2
- Every structure of UniProt P48047
- Elsewhere: RCSB PDB 8H9L · PDBe 8H9L · UniProt P25705 · UniProt P06576 · UniProt P36542 · UniProt Q9UII2 · UniProt P48047
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