Research workbench
CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE
Analyse CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K93
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Rhizobium etli
- Molecule
- sugar kinase
- UniProt
- Q2KDX6
- Ligands
- 1Q8, ADN, K
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.5 · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | sugar kinase | protein | 330 | 44% helix, 22% strand | Q2KDX6 |
Ligands and binding sites
- 1Q8 · N-(hydroxymethyl)benzamide · ligand · 8 copies · chains A, B
- ADN · Adenosine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.78 | 0.87 | 60 | ADN |
| 2 | 410 | 0.77 | 0.86 | 58 | ADN |
| 3 | 677 | 0.74 | 0.80 | 66 | empty |
| 4 | 101 | 0.52 | 0.82 | 15 | DMS, 1Q8 |
| 5 | 122 | 0.49 | 0.79 | 17 | 1Q8, DMS |
Interfaces
1 interface between chains.
- A–B · 920 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4K93 · Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed… · 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 Q2KDX6
- Elsewhere: RCSB PDB 4K93 · PDBe 4K93 · UniProt Q2KDX6
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