Research workbench
Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor TP5A at 2.0 a resolution: implications for catalysis and azt activation
Analyse Crystal structure of yeast thymidylate kinase complexed with the bisubstrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TMK
- Type
- protein
- Length
- 1,711 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P00572
- Ligands
- T5A
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Thymidylate kinase (EC 2.7.4.9) | protein | 216 | 47% helix, 13% strand | P00572 |
| C | Thymidylate kinase (EC 2.7.4.9) | protein | 205 | 48% helix, 14% strand | P00572 |
| D, H | Thymidylate kinase (EC 2.7.4.9) | protein | 214 | 48% helix, 14% strand | P00572 |
| E, G | Thymidylate kinase (EC 2.7.4.9) | protein | 215 | 47% helix, 14% strand | P00572 |
Ligands and binding sites
- T5A · P1-(5'-adenosyl)p5-(5'-thymidyl)pentaphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.68 | 0.87 | 34 | T5A |
| 2 | 194 | 0.68 | 0.87 | 34 | T5A |
| 3 | 189 | 0.68 | 0.86 | 32 | T5A |
| 4 | 146 | 0.65 | 0.87 | 25 | T5A |
| 5 | 265 | 0.65 | 0.82 | 38 | T5A |
Interfaces
10 interfaces between chains.
- E–F · 884 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 880 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 856 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 380 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3TMK · Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor… · the same entry in another collection · chain H against H, TM-score 1.00
- P00572 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P00572) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P00572
- Elsewhere: RCSB PDB 3TMK · PDBe 3TMK · UniProt P00572
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