Research workbench
Yeast thymidylate kinase complexed with 3'-azido-3'-deoxythymidine monophosphate (azt-mp)
Analyse Yeast thymidylate kinase complexed with 3'-azido-3'-deoxythymidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2TMK
- 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
- ATM, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 49% helix, 15% strand | P00572 |
Ligands and binding sites
- ATM · 3'-azido-3'-deoxythymidine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.65 | 0.86 | 29 | SO4, ATM |
| 2 | 155 | 0.65 | 0.86 | 26 | SO4, ATM |
| 3 | 64 | 0.35 | 0.77 | 16 | empty |
| 4 | 59 | 0.31 | 0.75 | 16 | empty |
| 5 | 68 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 944 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2TMK · Yeast thymidylate kinase complexed with 3'-azido-3'-deoxythymidine monophosphate (azt-mp) · 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 2TMK · PDBe 2TMK · UniProt P00572
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.