MolNFT v1 · #25257 · protein
Crystal structure of a putative thiamine BIOSYNTHESIS/SALVAGE protein (TM0486) from thermotoga maritima at 1.80 a resolution
1VK8 · Hypothetical protein TM0486: “Crystal structure of a putative thiamine BIOSYNTHESIS/SALVAGE protein (TM0486) from thermotoga maritima at…”. X-ray diffraction, 1 ligand (UNL), 5 pockets (best druggability 0.84). MolNFT v1 #25257 on…
- PDB
- 1VK8
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TM0486
- UniProt
- Q9WYV6
- Ligands
- UNL
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Hypothetical protein TM0486 | protein | 93 | 42% helix, 30% strand | Q9WYV6 |
| C | Hypothetical protein TM0486 | protein | 94 | 41% helix, 31% strand | Q9WYV6 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.84 | 0.98 | 32 | empty |
| 2 | 193 | 0.79 | 0.94 | 30 | UNL |
| 3 | 148 | 0.78 | 0.95 | 30 | UNL |
| 4 | 186 | 0.77 | 0.93 | 30 | UNL |
| 5 | 126 | 0.75 | 0.94 | 32 | UNL |
Interfaces
6 interfaces between chains.
- C–D · 1285 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1246 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 971 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 921 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1VK8 · Crystal structure of a putative thiamine BIOSYNTHESIS/SALVAGE protein (TM0486) from… · 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 Q9WYV6
- Elsewhere: RCSB PDB 1VK8 · PDBe 1VK8 · UniProt Q9WYV6
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