Research workbench
The crystal structure of thymidylate kinase from pseudomonas aeruginosa PAO1 in complex with azt 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
- 4GMD
- Type
- protein
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9HZN8
- Ligands
- ATM, CA, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 203 | 57% helix, 13% strand | Q9HZN8 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 195 | 54% helix, 14% strand | Q9HZN8 |
| C | Thymidylate kinase (EC 2.7.4.9) | protein | 197 | 55% helix, 14% strand | Q9HZN8 |
| D | Thymidylate kinase (EC 2.7.4.9) | protein | 196 | 55% helix, 14% strand | Q9HZN8 |
Ligands and binding sites
- ATM · 3'-azido-3'-deoxythymidine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.76 | 0.88 | 42 | empty |
| 2 | 374 | 0.70 | 0.82 | 45 | ATM |
| 3 | 367 | 0.70 | 0.83 | 28 | empty |
| 4 | 261 | 0.66 | 0.82 | 37 | ATM, CL |
| 5 | 229 | 0.66 | 0.83 | 32 | ATM, CL |
Interfaces
6 interfaces between chains.
- B–D · 1178 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1171 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 365 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 297 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GMD · The crystal structure of thymidylate kinase from Pseudomonas aeruginosa PAO1 in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HZN8 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9HZN8) · 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 Q9HZN8
- Elsewhere: RCSB PDB 4GMD · PDBe 4GMD · UniProt Q9HZN8
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