Research workbench
Chloroplast ATP synthase (O2, CF1)
Analyse Chloroplast ATP synthase (O2, CF1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VOG
- Type
- protein
- Length
- 3,562 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
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 8 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 496 | 43% helix, 15% strand | P06450 |
| B, C | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 501 | 41% helix, 15% strand | P06450 |
| D | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 478 | 36% helix, 18% strand | P00825 |
| E | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 479 | 37% helix, 18% strand | P00825 |
| F | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 478 | 36% helix, 16% strand | P00825 |
| d | ATP synthase delta chain, chloroplastic | protein | 178 | 62% helix, 7% strand | P11402 |
| g | ATP synthase gamma chain, chloroplastic | protein | 321 | 53% helix, 12% strand | P05435 |
| e | ATP synthase epsilon chain, chloroplastic | protein | 130 | 26% helix, 28% 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 · chains C, E
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 | 956 | 0.89 | 0.91 | 138 | ATP |
| 2 | 952 | 0.89 | 0.90 | 129 | ATP |
| 3 | 774 | 0.82 | 0.86 | 87 | ATP |
| 4 | 386 | 0.82 | 0.91 | 64 | ADP |
| 5 | 625 | 0.82 | 0.87 | 73 | ATP |
Interfaces
19 interfaces between chains.
- C–E · 3023 Ų buried · 46 hydrogen bonds · protein-protein
- B–E · 2606 Ų buried · 33 hydrogen bonds · protein-protein
- A–F · 2510 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 2423 Ų buried · 43 hydrogen bonds · protein-protein
- C–F · 2417 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VOG · Chloroplast ATP synthase (O2, CF1) · the same entry in another collection · chain d against d, TM-score 1.00
- 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
- 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 0.96
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 6VOG · PDBe 6VOG · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P05435 · UniProt P00833
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