Research workbench
Chloroplast ATP synthase (C1, CF1)
Analyse Chloroplast ATP synthase (C1, CF1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VMD
- Type
- protein
- Length
- 3,576 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, P00833, P05435
- Ligands
- ATP, ADP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 501 | 41% helix, 15% strand | P06450 |
| B | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 503 | 38% helix, 13% strand | P06450 |
| C | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 500 | 42% helix, 15% strand | P06450 |
| D | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 478 | 34% helix, 14% strand | P00825 |
| E | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 481 | 36% helix, 15% strand | P00825 |
| F | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 480 | 34% helix, 16% strand | P00825 |
| d | ATP synthase delta chain, chloroplastic | protein | 179 | 60% helix, 11% strand | P11402 |
| e | ATP synthase epsilon chain, chloroplastic | protein | 131 | 27% helix, 24% strand | P00833 |
| g | ATP synthase gamma chain, chloroplastic | protein | 323 | 53% helix, 12% strand | P05435 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, D, B, E, C, F
- ADP · Adenosine-5'-diphosphate · 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 | 1141 | 0.87 | 0.88 | 124 | empty |
| 2 | 702 | 0.86 | 0.90 | 104 | ATP |
| 3 | 990 | 0.86 | 0.87 | 113 | ATP |
| 4 | 934 | 0.84 | 0.86 | 103 | ATP |
| 5 | 383 | 0.83 | 0.92 | 57 | empty |
Interfaces
18 interfaces between chains.
- A–F · 3051 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 2518 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 2416 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 2367 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 2094 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VMD · Chloroplast ATP synthase (C1, CF1) · the same entry in another collection · chain g against g, 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 E 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 P00833
- Every structure of UniProt P05435
- Elsewhere: RCSB PDB 6VMD · PDBe 6VMD · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P00833 · UniProt P05435
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