MolNFT v1 · #139208 · protein
K16M mutant of thermus thermophilus HB8 thymidylate kinase
5X8J: “K16M mutant of thermus thermophilus HB8 thymidylate kinase”. X-ray diffraction, 4 pockets (best druggability 0.44). MolNFT v1 #139208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X8J
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q5SHX3
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 184 | 53% helix, 15% strand | Q5SHX3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 185 | 55% helix, 15% strand | Q5SHX3 |
Ligands and binding sites
- FMT · Formic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.44 | 0.76 | 26 | FMT |
| 2 | 110 | 0.41 | 0.76 | 22 | empty |
| 3 | 58 | 0.39 | 0.80 | 14 | empty |
| 4 | 56 | 0.36 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1070 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 Q5SHX3
- Elsewhere: RCSB PDB 5X8J · PDBe 5X8J · UniProt Q5SHX3
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