Research workbench
The crystal structure of thymidylate kinase from pseudomonas aeruginosa PAO1 in complex with thymidine monophosphate.
Analyse The crystal structure of thymidylate kinase from pseudomonas aeruginosa PAO1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E5U
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9HZN8
- Ligands
- TMP, CA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 58% helix, 13% strand | Q9HZN8 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 206 | 55% helix, 13% strand | Q9HZN8 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 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 | 378 | 0.70 | 0.82 | 38 | TMP, CA |
| 2 | 413 | 0.68 | 0.80 | 35 | TMP, CA |
Interfaces
1 interface between chains.
- A–B · 1178 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4E5U · The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZN8 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9HZN8) · a predicted model of the same protein · chain A 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 Q9HZN8
- Elsewhere: RCSB PDB 4E5U · PDBe 4E5U · UniProt Q9HZN8
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