Research workbench
Structure of hydroxyethylthiazole kinase thim from staphylococcus aureus in complex with substrate analog 2-(1,3,5-trimethyl-1H- pyrazole-4-YL)ETHANOL
Analyse Structure of hydroxyethylthiazole kinase thim from staphylococcus aureus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CGA
- Type
- protein
- Length
- 1,498 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyethylthiazole kinase
- EC
- 2.7.1.50
- UniProt
- Q6GEY3
- Ligands
- KP6, MG
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 252 | 55% helix, 17% strand | Q6GEY3 |
| B | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 249 | 56% helix, 16% strand | Q6GEY3 |
| C | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 251 | 56% helix, 16% strand | Q6GEY3 |
| E | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 255 | 55% helix, 17% strand | Q6GEY3 |
| F | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 245 | 56% helix, 15% strand | Q6GEY3 |
| H | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 246 | 57% helix, 15% strand | Q6GEY3 |
Ligands and binding sites
- KP6 · 2-(1,3,5-trimethyl-1H-pyrazol-4-yl)ethanol · ligand · 6 copies · chains A, B, C, E, F, H
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.85 | 0.95 | 48 | empty |
| 2 | 342 | 0.85 | 0.94 | 48 | empty |
| 3 | 944 | 0.83 | 0.84 | 114 | empty |
| 4 | 359 | 0.79 | 0.89 | 48 | empty |
| 5 | 520 | 0.68 | 0.79 | 43 | KP6, MG |
Interfaces
9 interfaces between chains.
- B–C · 1000 Ų buried · 18 hydrogen bonds · protein-protein
- E–H · 989 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 988 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 981 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 973 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5CGA · Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with… · the same entry in another collection · chain H against H, TM-score 1.00
- Q6GEY3 · AlphaFold monomer V2.0 prediction for hydroxyethylthiazole kinase (Q6GEY3) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q6GEY3
- Elsewhere: RCSB PDB 5CGA · PDBe 5CGA · UniProt Q6GEY3
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