MolNFT v1 · #25417 · protein
Crystal structure of thiamine monophosphate kinase (thil) from aquifex aeolicus
1VQV: “Crystal structure of thiamine monophosphate kinase (thil) from aquifex aeolicus”. X-ray diffraction, 1 ligand (PO4), 6 pockets (best druggability 0.70). MolNFT v1 #25417 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VQV
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamine monophosphate kinase
- EC
- 2.7.4.16
- UniProt
- O67883
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 292 | 36% helix, 25% strand | O67883 |
| B | Thiamine monophosphate kinase (EC 2.7.4.16) | protein | 295 | 39% helix, 25% strand | O67883 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.70 | 0.77 | 71 | empty |
| 2 | 576 | 0.66 | 0.77 | 58 | empty |
| 3 | 134 | 0.54 | 0.81 | 21 | empty |
| 4 | 55 | 0.35 | 0.79 | 14 | empty |
| 5 | 63 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2465 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 1VQV · Crystal Structure of Thiamine Monophosphate Kinase (thil) from Aquifex Aeolicus · the same entry in another collection · chain A against A, TM-score 1.00
- O67883 · AlphaFold monomer V2.0 prediction for thiamine-monophosphate kinase (O67883) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O67883
- Elsewhere: RCSB PDB 1VQV · PDBe 1VQV · UniProt O67883
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