MolNFT v1 · #31865 · protein
Crystal structure of thymidine kinase from U.UREALYTICUM in complex with thymidine
2B8T: “Crystal structure of thymidine kinase from U.UREALYTICUM in complex with thymidine”. X-ray diffraction, 2 ligands (THM, ZN), 10 pockets (best druggability 0.79). MolNFT v1 #31865 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2B8T
- Type
- protein
- Length
- 798 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- Q9PPP5
- Ligands
- THM, ZN
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 206 | 28% helix, 22% strand | Q9PPP5 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 189 | 28% helix, 23% strand | Q9PPP5 |
| C | Thymidine kinase (EC 2.7.1.21) | protein | 199 | 27% helix, 24% strand | Q9PPP5 |
| D | Thymidine kinase (EC 2.7.1.21) | protein | 204 | 25% helix, 25% strand | Q9PPP5 |
Ligands and binding sites
- THM · Thymidine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.79 | 0.81 | 91 | THM, TRS |
| 2 | 624 | 0.76 | 0.82 | 82 | empty |
| 3 | 151 | 0.69 | 0.89 | 25 | empty |
| 4 | 610 | 0.69 | 0.77 | 62 | THM |
| 5 | 153 | 0.68 | 0.88 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2189 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 2109 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1118 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 819 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2B8T · Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine · the same entry in another collection · chain D against D, TM-score 1.00
- Q9PPP5 · AlphaFold monomer V2.0 prediction for thymidine kinase (Q9PPP5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9PPP5
- Elsewhere: RCSB PDB 2B8T · PDBe 2B8T · UniProt Q9PPP5
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