Research workbench
Mutation of THR163 to ser in human thymidine kinase shifts the specificity from thymidine towards the nucleoside analogue azidothymidine
Analyse Mutation of THR163 to ser in human thymidine kinase shifts the specificity from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WVJ
- Type
- protein
- Length
- 1,290 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase, cytosolic
- EC
- 2.7.1.21
- UniProt
- P04183
- Ligands
- TTP, ZN, MG
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Thymidine kinase, cytosolic (EC 2.7.1.21) | protein | 160 | 29% helix, 26% strand | P04183 |
| B | Thymidine kinase, cytosolic (EC 2.7.1.21) | protein | 161 | 30% helix, 26% strand | P04183 |
| D | Thymidine kinase, cytosolic (EC 2.7.1.21) | protein | 162 | 28% helix, 27% strand | P04183 |
| G | Thymidine kinase, cytosolic (EC 2.7.1.21) | protein | 161 | 29% helix, 27% strand | P04183 |
| H | Thymidine kinase, cytosolic (EC 2.7.1.21) | protein | 166 | 28% helix, 27% strand | P04183 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, D, C, E, G, F, H
- MG · Magnesium ion · metal · 3 copies · chains D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.82 | 0.83 | 118 | empty |
| 2 | 770 | 0.78 | 0.82 | 86 | empty |
| 3 | 632 | 0.75 | 0.81 | 70 | empty |
| 4 | 360 | 0.71 | 0.83 | 47 | TTP, MG |
| 5 | 315 | 0.68 | 0.82 | 42 | TTP, MG |
Interfaces
15 interfaces between chains.
- F–H · 1299 Ų buried · 29 hydrogen bonds · protein-protein
- E–G · 1291 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1271 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1268 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 845 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2WVJ · Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine… · the same entry in another collection · chain F against F, TM-score 1.00
- P04183 · AlphaFold monomer V2.0 prediction for thymidine kinase, cytosolic (P04183) · a predicted model of the same protein · 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 P04183
- Elsewhere: RCSB PDB 2WVJ · PDBe 2WVJ · UniProt P04183
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