MolNFT v1 · #115598 · protein
Structure of hydroxyethylthiazole kinase thim from staphylococcus aureus in complex with native substrate 2-(4-methyl-1,3-thiazol-5- YL)ETHANOL.
5COJ: “Structure of hydroxyethylthiazole kinase thim from staphylococcus aureus in complex with native substrate…”. X-ray diffraction, 2 ligands (TZE, MG), 13 pockets (best druggability 0.85). MolNFT v1 #115598 on GenesisL1: 3D structure…
- PDB
- 5COJ
- Type
- protein
- Length
- 1,486 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
- TZE, MG
- Pockets
- 13 · 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 | 248 | 56% helix, 16% strand | Q6GEY3 |
| C | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 249 | 55% helix, 16% strand | Q6GEY3 |
| E | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 252 | 54% helix, 17% strand | Q6GEY3 |
| F | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 241 | 56% helix, 15% strand | Q6GEY3 |
| H | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 244 | 57% helix, 15% strand | Q6GEY3 |
Ligands and binding sites
- TZE · 2-(4-methyl-thiazol-5-yl)-ethanol · ligand · 6 copies · chains A, C, B, 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
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.85 | 0.95 | 48 | empty |
| 2 | 339 | 0.84 | 0.94 | 48 | empty |
| 3 | 1086 | 0.80 | 0.82 | 110 | empty |
| 4 | 345 | 0.78 | 0.88 | 56 | empty |
| 5 | 545 | 0.69 | 0.79 | 52 | TZE, MG |
Interfaces
9 interfaces between chains.
- B–C · 1012 Ų buried · 20 hydrogen bonds · protein-protein
- E–H · 1002 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 992 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 978 Ų buried · 21 hydrogen bonds · protein-protein
- F–H · 975 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5COJ · 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 H 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 Q6GEY3
- Elsewhere: RCSB PDB 5COJ · PDBe 5COJ · UniProt Q6GEY3
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