MolNFT v1 · #167561 · protein
Chloroplast ATP synthase (R2, CF1)
6VOM · ATP synthase subunit alpha, chloroplastic: “Chloroplast ATP synthase (R2, CF1)”. Electron microscopy, 3 ligands (ATP, ADP, TTX), 20 pockets (best druggability 0.87). MolNFT v1 #167561 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6VOM
- Type
- protein
- Length
- 3,566 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha, chloroplastic; ATP synthase subunit beta, chloroplastic; ATP…
- EC
- 7.1.2.2
- UniProt
- P06450, P00825, P11402, P05435, P00833
- Ligands
- ATP, ADP, TTX
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 497 | 40% helix, 16% strand | P06450 |
| B | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 501 | 41% helix, 19% strand | P06450 |
| C | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 500 | 42% helix, 16% strand | P06450 |
| D | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 479 | 37% helix, 20% strand | P00825 |
| E | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 480 | 38% helix, 19% strand | P00825 |
| F | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 478 | 38% helix, 18% strand | P00825 |
| d | ATP synthase delta chain, chloroplastic | protein | 179 | 61% helix, 13% strand | P11402 |
| g | ATP synthase gamma chain, chloroplastic | protein | 321 | 55% helix, 14% strand | P05435 |
| e | ATP synthase epsilon chain, chloroplastic | protein | 131 | 28% helix, 24% strand | P00833 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains D, C, E
- TTX · Tentoxin · ligand · chains A, 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 | 910 | 0.87 | 0.89 | 99 | ATP |
| 2 | 1031 | 0.87 | 0.88 | 114 | ATP |
| 3 | 593 | 0.87 | 0.92 | 82 | empty |
| 4 | 840 | 0.86 | 0.88 | 81 | ATP |
| 5 | 1033 | 0.84 | 0.85 | 93 | TTX |
Interfaces
20 interfaces between chains.
- C–E · 2981 Ų buried · 47 hydrogen bonds · protein-protein
- B–E · 2372 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2287 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 2271 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1971 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6VOM · Chloroplast ATP synthase (R2, CF1) · the same entry in another collection · chain e against e, TM-score 1.00
- P00825 · AlphaFold monomer V2.0 prediction for ATP synthase subunit beta, chloroplastic (P00825) · a predicted model of the same protein · chain D against A, TM-score 0.97
- P06450 · AlphaFold monomer V2.0 prediction for ATP synthase subunit alpha, chloroplastic (P06450) · a predicted model of the same protein · chain C 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 P06450
- Every structure of UniProt P00825
- Every structure of UniProt P11402
- Every structure of UniProt P05435
- Every structure of UniProt P00833
- Elsewhere: RCSB PDB 6VOM · PDBe 6VOM · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P05435 · UniProt P00833
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.