Research workbench
Y162F mutant of thermus thermophilus HB8 thymidylate kinase
Analyse Y162F mutant of thermus thermophilus HB8 thymidylate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X98
- Type
- protein
- Length
- 372 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
- Ligands
- MG
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 187 | 54% helix, 15% strand | Q5SHX3 |
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 185 | 53% helix, 15% strand | Q5SHX3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains B, A
- FMT · Formic acid · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.54 | 0.77 | 26 | empty |
| 2 | 165 | 0.47 | 0.76 | 24 | empty |
| 3 | 74 | 0.46 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1070 Ų buried · 16 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 5X98 · PDBe 5X98 · UniProt Q5SHX3
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