Research workbench
Chloroplast ATP synthase (R2, CF1FO)
Analyse Chloroplast ATP synthase (R2, CF1FO) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VOL
- Type
- protein
- Length
- 5,165 residues
- Chains
- 26
- 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, P06453, P31853, P06451, P69447
- Ligands
- ATP, ADP, TTX
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 13 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 497 | 41% helix, 16% strand | P06450 |
| B | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 501 | 42% helix, 17% strand | P06450 |
| C | ATP synthase subunit alpha, chloroplastic (EC 7.1.2.2) | protein | 500 | 44% helix, 18% strand | P06450 |
| D | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 479 | 37% helix, 19% strand | P00825 |
| E | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 480 | 38% helix, 20% strand | P00825 |
| F | ATP synthase subunit beta, chloroplastic (EC 7.1.2.2) | protein | 478 | 36% helix, 18% strand | P00825 |
| d | ATP synthase delta chain, chloroplastic | protein | 179 | 63% helix, 12% strand | P11402 |
| g | ATP synthase gamma chain, chloroplastic | protein | 321 | 56% helix, 12% strand | P05435 |
| e | ATP synthase epsilon chain, chloroplastic | protein | 131 | 31% helix, 31% strand | P00833 |
| I | ATP synthase subunit B, chloroplastic | protein | 150 | 97% helix, 0% strand | P06453 |
| J | ATP synthase subunit B', chloroplastic | protein | 133 | 92% helix, 0% strand | P31853 |
| a | ATP synthase subunit a, chloroplastic | protein | 210 | 75% helix, 0% strand | P06451 |
| M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z | ATP synthase subunit C, chloroplastic | protein | 79 | 85% helix, 0% strand | P69447 |
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 | 771 | 0.87 | 0.90 | 107 | ATP |
| 2 | 796 | 0.87 | 0.90 | 93 | ATP |
| 3 | 655 | 0.86 | 0.90 | 75 | ATP |
| 4 | 1061 | 0.84 | 0.85 | 103 | TTX |
| 5 | 807 | 0.83 | 0.86 | 100 | empty |
Interfaces
60 interfaces between chains.
- C–E · 3089 Ų buried · 41 hydrogen bonds · protein-protein
- B–E · 2364 Ų buried · 31 hydrogen bonds · protein-protein
- A–F · 2340 Ų buried · 32 hydrogen bonds · protein-protein
- C–F · 2288 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 2192 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VOL · Chloroplast ATP synthase (R2, CF1FO) · the same entry in another collection · chain I against I, TM-score 1.00
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
- Every structure of UniProt P06453
- Every structure of UniProt P31853
- Every structure of UniProt P06451
- Every structure of UniProt P69447
- Elsewhere: RCSB PDB 6VOL · PDBe 6VOL · UniProt P06450 · UniProt P00825 · UniProt P11402 · UniProt P05435 · UniProt P00833 · UniProt P06453 · UniProt P31853 · UniProt P06451 · UniProt P69447
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