Research workbench
PS3 F1-ATPase pi-bound dwell
Analyse PS3 F1-ATPase pi-bound dwell in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L1S
- Type
- protein
- Length
- 3,118 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain
- EC
- 7.1.2.2
- UniProt
- A0A0M3VGF9, A0A0M4U1P9, A0A0M4TPJ7
- Ligands
- ATP, MG, PO4
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 474 | 41% helix, 20% strand | A0A0M3VGF9 |
| B | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 475 | 41% helix, 19% strand | A0A0M3VGF9 |
| C | ATP synthase subunit alpha (EC 7.1.2.2) | protein | 476 | 40% helix, 19% strand | A0A0M3VGF9 |
| D | ATP synthase subunit beta (EC 7.1.2.2) | protein | 470 | 39% helix, 21% strand | A0A0M4U1P9 |
| E | ATP synthase subunit beta (EC 7.1.2.2) | protein | 470 | 38% helix, 20% strand | A0A0M4U1P9 |
| F | ATP synthase subunit beta (EC 7.1.2.2) | protein | 471 | 38% helix, 20% strand | A0A0M4U1P9 |
| G | ATP synthase gamma chain | protein | 282 | 61% helix, 12% strand | A0A0M4TPJ7 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains A, D, B, E, C, F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- PO4 · Phosphate ion · ion · chains A, 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 | 890 | 0.86 | 0.88 | 94 | ATP, MG |
| 2 | 1109 | 0.86 | 0.87 | 108 | ATP, MG |
| 3 | 412 | 0.84 | 0.92 | 62 | ATP, MG |
| 4 | 366 | 0.84 | 0.93 | 65 | empty |
| 5 | 808 | 0.83 | 0.85 | 89 | ATP, MG |
Interfaces
13 interfaces between chains.
- C–D · 2898 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 2195 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2143 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 2142 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 2021 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7L1S · PS3 F1-ATPase Pi-bound Dwell · the same entry in another collection · chain A against A, 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 A0A0M3VGF9
- Every structure of UniProt A0A0M4U1P9
- Every structure of UniProt A0A0M4TPJ7
- Elsewhere: RCSB PDB 7L1S · PDBe 7L1S · UniProt A0A0M3VGF9 · UniProt A0A0M4U1P9 · UniProt A0A0M4TPJ7
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