MolNFT v1 · #22993 · protein
Yeast thymidylate kinase complexed with thymidine monophosphate (dtmp)
1TMK: “Yeast thymidylate kinase complexed with thymidine monophosphate (dtmp)”. X-ray diffraction, 2 ligands (TMP, SO4), 4 pockets (best druggability 0.64). MolNFT v1 #22993 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1TMK
- Type
- protein
- Length
- 408 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P00572
- Ligands
- TMP, SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 48% helix, 14% strand | P00572 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.64 | 0.87 | 26 | TMP |
| 2 | 149 | 0.63 | 0.86 | 29 | SO4, TMP |
| 3 | 61 | 0.33 | 0.76 | 14 | empty |
| 4 | 51 | 0.31 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1TMK · Yeast thymidylate kinase complexed with thymidine monophosphate (dtmp) · the same entry in another collection · chain A against A, TM-score 1.00
- P00572 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P00572) · 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 P00572
- Elsewhere: RCSB PDB 1TMK · PDBe 1TMK · UniProt P00572
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