Research workbench
E. COLI ATP synthase state 1D
Analyse E. COLI ATP synthase state 1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OQU
- Type
- protein
- Length
- 4,851 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit delta; ATP synthase subunit alpha; ATP synthase subunit B; ATP…
- EC
- 7.1.2.2
- UniProt
- V0ZA15, A0A073FQ32, A0A073FPT7, A0A4V1DSB5, J7RYJ3, A0A0F6CB56, F4TL55, C3SL77
- Ligands
- ATP, ADP, MG, PO4
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 12 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | ATP synthase subunit delta | protein | 173 | 54% helix, 14% strand | V0ZA15 |
| C | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 512 | 42% helix, 18% strand | A0A073FQ32 |
| B | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 513 | 41% helix, 20% strand | A0A073FQ32 |
| A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 508 | 42% helix, 20% strand | A0A073FQ32 |
| X, Y | ATP synthase subunit B | protein | 156 | 89% helix, 0% strand | A0A073FPT7 |
| H | ATP synthase epsilon chain | protein | 136 | 24% helix, 35% strand | A0A4V1DSB5 |
| G | ATP synthase gamma chain | protein | 284 | 61% helix, 15% strand | J7RYJ3 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 458 | 37% helix, 21% strand | A0A0F6CB56 |
| E, D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 460 | 37% helix, 20% strand | A0A0F6CB56 |
| J, L, M, N, O, P, Q, I, S | ATP synthase subunit C | protein | 77 | 90% helix, 0% strand | F4TL55 |
| R | ATP synthase subunit C | protein | 76 | 91% helix, 0% strand | F4TL55 |
| a | ATP synthase subunit a | protein | 266 | 73% helix, 3% strand | C3SL77 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains C, F, B, E, A, D
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, F, E, C, D
- MG · Magnesium ion · metal · 5 copies · chains C, B, A, F, D
- PO4 · Phosphate ion · ion · chains C, 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 | 1192 | 0.87 | 0.89 | 127 | ATP, MG |
| 2 | 1197 | 0.87 | 0.88 | 152 | ATP, MG |
| 3 | 907 | 0.84 | 0.86 | 99 | ATP, MG |
| 4 | 627 | 0.84 | 0.88 | 85 | ADP |
| 5 | 552 | 0.84 | 0.89 | 75 | empty |
Interfaces
58 interfaces between chains.
- X–Y · 2774 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 2574 Ų buried · 27 hydrogen bonds · protein-protein
- H–G · 2507 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2450 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 2358 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6OQU · E. coli ATP synthase State 1d · the same entry in another collection · chain W against W, 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 V0ZA15
- Every structure of UniProt A0A073FQ32
- Every structure of UniProt A0A073FPT7
- Every structure of UniProt A0A4V1DSB5
- Every structure of UniProt J7RYJ3
- Every structure of UniProt A0A0F6CB56
- Every structure of UniProt F4TL55
- Every structure of UniProt C3SL77
- Elsewhere: RCSB PDB 6OQU · PDBe 6OQU · UniProt V0ZA15 · UniProt A0A073FQ32 · UniProt A0A073FPT7 · UniProt A0A4V1DSB5 · UniProt J7RYJ3 · UniProt A0A0F6CB56 · UniProt F4TL55 · UniProt C3SL77
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