MolNFT v1 · #92893 · protein
The crystal structure of thymidylate kinase from pseudomonas aeruginosa PAO1 in complex with azt monophosphate
4GMD: “The crystal structure of thymidylate kinase from pseudomonas aeruginosa PAO1 in complex with azt monophosphate”. X-ray diffraction, 3 ligands (ATM, CA, CL), 7 pockets (best druggability 0.76). MolNFT v1 #92893 on GenesisL1: 3D…
- 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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