Research workbench
Crystal structure of the 5-(hydroxyethyl)-methylthiazole kinase thim from klebsiella pneumonia in complex with tze
Analyse Crystal structure of the 5-(hydroxyethyl)-methylthiazole kinase thim from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K28
- Type
- protein
- Length
- 706 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyethylthiazole kinase
- EC
- 2.7.1.50
- UniProt
- W9BB97
- Ligands
- TZE, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 235 | 55% helix, 14% strand | W9BB97 |
| B | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 232 | 58% helix, 14% strand | W9BB97 |
| C | Hydroxyethylthiazole kinase (EC 2.7.1.50) | protein | 239 | 55% helix, 16% strand | W9BB97 |
Ligands and binding sites
- TZE · 2-(4-methyl-thiazol-5-yl)-ethanol · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.83 | 0.94 | 30 | empty |
| 2 | 561 | 0.72 | 0.80 | 44 | TZE, MG |
| 3 | 319 | 0.71 | 0.84 | 48 | empty |
| 4 | 571 | 0.71 | 0.79 | 50 | TZE |
| 5 | 595 | 0.70 | 0.79 | 44 | TZE, MG |
Interfaces
3 interfaces between chains.
- A–C · 1049 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1043 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1011 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6K28 · Crystal structure of the 5-(Hydroxyethyl)-methylthiazole Kinase ThiM from Klebsiella… · the same entry in another collection · chain A 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 W9BB97
- Elsewhere: RCSB PDB 6K28 · PDBe 6K28 · UniProt W9BB97
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