Research workbench
Thymidine kinase from thermotoga maritima in complex with thymidine + appnhp
Analyse Thymidine kinase from thermotoga maritima in complex with thymidine + appnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QQ0
- Type
- protein
- Length
- 339 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- Q9WYN2
- Ligands
- THM, ANP, TMP, ADP, ZN, MG
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 169 | 30% helix, 28% strand | Q9WYN2 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 170 | 29% helix, 26% strand | Q9WYN2 |
Ligands and binding sites
- THM · Thymidine · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- TMP · Thymidine-5'-phosphate · ligand · chains B
- ADP · Adenosine-5'-diphosphate · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.64 | 0.83 | 32 | MG, TMP |
| 2 | 192 | 0.60 | 0.82 | 34 | MG, THM, ANP |
Interfaces
1 interface between chains.
- A–B · 1133 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2QQ0 · Thymidine Kinase from Thermotoga Maritima in complex with thymidine + AppNHp · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYN2 · AlphaFold monomer V2.0 prediction for thymidine kinase (Q9WYN2) · a predicted model of the same protein · chain A 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 Q9WYN2
- Elsewhere: RCSB PDB 2QQ0 · PDBe 2QQ0 · UniProt Q9WYN2
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