MolNFT v1 · #122268 · protein
Caldalaklibacillus thermarum F1-ATPase (epsilon mutant)
5IK2 · ATP synthase subunit alpha: “Caldalaklibacillus thermarum F1-ATPase (epsilon mutant)”. X-ray diffraction, 3 ligands (ADP, MG, PO4), 20 pockets (best druggability 0.88). MolNFT v1 #122268 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IK2
- Type
- protein
- Length
- 6,445 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP synthase subunit alpha; ATP synthase subunit beta; ATP synthase gamma chain; ATP…
- EC
- 3.6.3.14
- UniProt
- F5LA74, F5LA72, F5LA73, F5LA71
- Ligands
- ADP, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 10 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 475 | 40% helix, 19% strand | F5LA74 |
| B | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 469 | 39% helix, 21% strand | F5LA74 |
| C | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 475 | 40% helix, 19% strand | F5LA74 |
| D | ATP synthase subunit beta (EC 3.6.3.14) | protein | 461 | 39% helix, 22% strand | F5LA72 |
| E, F, L, M, N | ATP synthase subunit beta (EC 3.6.3.14) | protein | 462 | 40% helix, 21% strand | F5LA72 |
| G, O | ATP synthase gamma chain | protein | 285 | 62% helix, 13% strand | F5LA73 |
| H | ATP synthase epsilon chain | protein | 132 | 29% helix, 45% strand | F5LA71 |
| J | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 468 | 40% helix, 21% strand | F5LA74 |
| K | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 476 | 39% helix, 20% strand | F5LA74 |
| P | ATP synthase epsilon chain | protein | 134 | 29% helix, 44% strand | F5LA71 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, D, B, E, C, F, I, L, J, M, K, N
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, F, I, J, K, L, N
- PO4 · Phosphate ion · ion · 2 copies · chains A, E, I, M
- GOL · Glycerol · additive · 16 copies · chains A, E, B, C, F, I, M, J, K, N
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 | 1128 | 0.88 | 0.90 | 146 | ADP, MG |
| 2 | 922 | 0.88 | 0.90 | 110 | ADP, MG |
| 3 | 918 | 0.87 | 0.89 | 101 | ADP, MG |
| 4 | 492 | 0.85 | 0.91 | 72 | empty |
| 5 | 544 | 0.84 | 0.90 | 63 | ADP, MG |
Interfaces
36 interfaces between chains.
- K–L · 2967 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2836 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 2260 Ų buried · 23 hydrogen bonds · protein-protein
- I–L · 2231 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 2222 Ų buried · 28 hydrogen bonds · protein-protein
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 F5LA74
- Every structure of UniProt F5LA72
- Every structure of UniProt F5LA73
- Every structure of UniProt F5LA71
- Elsewhere: RCSB PDB 5IK2 · PDBe 5IK2 · UniProt F5LA74 · UniProt F5LA72 · UniProt F5LA73 · UniProt F5LA71
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