Research workbench
Crystal structure of thymidylate kinase from burkholderia thailandensis
Analyse Crystal structure of thymidylate kinase from burkholderia thailandensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V9P
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q2SWM4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 199 | 57% helix, 13% strand | Q2SWM4 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 202 | 56% helix, 13% strand | Q2SWM4 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.73 | 0.77 | 85 | GOL, PEG |
| 2 | 206 | 0.62 | 0.83 | 24 | MRD, ACT |
| 3 | 207 | 0.61 | 0.82 | 26 | MRD, ACT |
| 4 | 79 | 0.30 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 492 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3V9P · Crystal structure of Thymidylate kinase from Burkholderia thailandensis · the same entry in another collection · chain A against A, TM-score 1.00
- Q2SWM4 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q2SWM4) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q2SWM4
- Elsewhere: RCSB PDB 3V9P · PDBe 3V9P · UniProt Q2SWM4
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