Research workbench
Caldalaklibacillus thermarum F1-ATPase (wild type)
Analyse Caldalaklibacillus thermarum F1-ATPase (wild type) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HKK
- Type
- protein
- Length
- 6,451 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, ATP, MG, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 475 | 42% helix, 20% strand | F5LA74 |
| B, J | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 475 | 41% helix, 20% strand | F5LA74 |
| C | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 476 | 41% helix, 20% strand | F5LA74 |
| D, E, F, L, M, N | ATP synthase subunit beta (EC 3.6.3.14) | protein | 461 | 40% helix, 22% strand | F5LA72 |
| G, O | ATP synthase gamma chain | protein | 284 | 63% helix, 13% strand | F5LA73 |
| H, P | ATP synthase epsilon chain | protein | 132 | 30% helix, 45% strand | F5LA71 |
| I | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 474 | 42% helix, 20% strand | F5LA74 |
| K | ATP synthase subunit alpha (EC 3.6.3.14) | protein | 478 | 41% helix, 20% strand | F5LA74 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, D, B, E, C, F, I, L, J, M, K, N
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains G, H, O, P
- MG · Magnesium ion · metal · 12 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 · 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 | 982 | 0.88 | 0.90 | 116 | empty |
| 2 | 956 | 0.88 | 0.90 | 132 | ADP, MG |
| 3 | 1153 | 0.86 | 0.87 | 101 | empty |
| 4 | 689 | 0.82 | 0.86 | 62 | empty |
| 5 | 899 | 0.82 | 0.84 | 93 | ADP, MG |
Interfaces
36 interfaces between chains.
- K–L · 3058 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 3030 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 2299 Ų buried · 21 hydrogen bonds · protein-protein
- I–L · 2262 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 2246 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5HKK · Caldalaklibacillus thermarum F1-ATPase (wild type) · 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 F5LA74
- Every structure of UniProt F5LA72
- Every structure of UniProt F5LA73
- Every structure of UniProt F5LA71
- Elsewhere: RCSB PDB 5HKK · PDBe 5HKK · UniProt F5LA74 · UniProt F5LA72 · UniProt F5LA73 · UniProt F5LA71
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