MolNFT v1 · #141541 · protein
Crystal structure of thymidylate kinase in complex with ADP and tdp from thermus thermophilus HB8
5ZB0: “Crystal structure of thymidylate kinase in complex with ADP and tdp from thermus thermophilus HB8”. X-ray diffraction, 4 ligands (TYD, ADP, MG), 2 pockets (best druggability 0.49). MolNFT v1 #141541 on GenesisL1: 3D structure…
- PDB
- 5ZB0
- Type
- protein
- Length
- 370 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
- TYD, ADP, MG, CL
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 187 | 52% helix, 15% strand | Q5SHX3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 183 | 56% helix, 15% strand | Q5SHX3 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.49 | 0.79 | 24 | TYD, MG |
| 2 | 196 | 0.49 | 0.76 | 25 | TYD, MG |
Interfaces
1 interface between chains.
- A–B · 1052 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5ZB0 · Crystal structure of thymidylate kinase in complex with ADP and TDP from thermus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SHX3 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q5SHX3) · a predicted model of the same protein · chain B 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 Q5SHX3
- Elsewhere: RCSB PDB 5ZB0 · PDBe 5ZB0 · UniProt Q5SHX3
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