MolNFT v1 · #168674 · protein
E. COLI ATP synthase state 3B
6WNR · ATP synthase subunit delta: “E. COLI ATP synthase state 3B”. Electron microscopy, 4 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #168674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WNR
- 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
- A0A073H3T8, A0A073FQ32, A0A073FPT7, S1HQ43, J7RYJ3, A0A192CEZ8, F4TL55, C3SL77
- Ligands
- ATP, ADP, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 8 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | ATP synthase subunit delta | protein | 173 | 58% helix, 12% strand | A0A073H3T8 |
| C, B, A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 512 | 41% helix, 20% strand | A0A073FQ32 |
| X, Y | ATP synthase subunit B | protein | 153 | 90% helix, 0% strand | A0A073FPT7 |
| H | ATP synthase epsilon chain | protein | 136 | 25% helix, 40% strand | S1HQ43 |
| G | ATP synthase gamma chain | protein | 284 | 63% helix, 15% strand | J7RYJ3 |
| F, E, D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 460 | 36% helix, 21% strand | A0A192CEZ8 |
| I, J, L, M, N, O, P, Q, R, S | ATP synthase subunit C | protein | 77 | 95% helix, 0% strand | F4TL55 |
| a | ATP synthase subunit a | protein | 266 | 75% helix, 3% strand | C3SL77 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains C, E, B, D, A, F
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, F, E, A, D
- MG · Magnesium ion · metal · 5 copies · chains C, E, B, D, A, F
- PO4 · Phosphate ion · ion · chains A, 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 | 961 | 0.88 | 0.90 | 104 | ATP, MG |
| 2 | 778 | 0.87 | 0.90 | 100 | ATP, MG |
| 3 | 1055 | 0.87 | 0.88 | 116 | ATP, MG |
| 4 | 491 | 0.84 | 0.91 | 69 | empty |
| 5 | 695 | 0.84 | 0.88 | 102 | empty |
Interfaces
59 interfaces between chains.
- C–F · 2846 Ų buried · 28 hydrogen bonds · protein-protein
- X–Y · 2694 Ų buried · 9 hydrogen bonds · protein-protein
- H–G · 2589 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 2504 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 2363 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6WNR · E. coli ATP synthase State 3b · 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 A0A073H3T8
- Every structure of UniProt A0A073FQ32
- Every structure of UniProt A0A073FPT7
- Every structure of UniProt S1HQ43
- Every structure of UniProt J7RYJ3
- Every structure of UniProt A0A192CEZ8
- Every structure of UniProt F4TL55
- Every structure of UniProt C3SL77
- Elsewhere: RCSB PDB 6WNR · PDBe 6WNR · UniProt A0A073H3T8 · UniProt A0A073FQ32 · UniProt A0A073FPT7 · UniProt S1HQ43 · UniProt J7RYJ3 · UniProt A0A192CEZ8 · UniProt F4TL55 · UniProt C3SL77
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