MolNFT v1 · #139202 · protein
Amppcp and tmp bound crystal structure of thymidylate kinase from thermus thermophilus HB8
5X8C: “Amppcp and tmp bound crystal structure of thymidylate kinase from thermus thermophilus HB8”. X-ray diffraction, 4 ligands (TMP, ACP, MG), 3 pockets (best druggability 0.52). MolNFT v1 #139202 on GenesisL1: 3D structure, binding…
- PDB
- 5X8C
- Type
- protein
- Length
- 375 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
- TMP, ACP, MG, CL
- Pockets
- 3 · best druggability 0.52
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 | 189 | 52% helix, 14% strand | Q5SHX3 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 186 | 55% helix, 15% strand | Q5SHX3 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 11 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.52 | 0.78 | 24 | TMP |
| 2 | 157 | 0.51 | 0.79 | 20 | TMP, MG |
| 3 | 53 | 0.38 | 0.81 | 14 | CL |
Interfaces
1 interface between chains.
- A–B · 1064 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5X8C · AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8 · 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 5X8C · PDBe 5X8C · UniProt Q5SHX3
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