Research workbench
Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with ethyl 3,4-diaminobenzoate
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
- 4K8T
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar kinase
- UniProt
- Q2KDX6
- Ligands
- ADN, E34, K
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 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
- ADN · Adenosine · ligand · 2 copies · chains A, B
- E34 · ethyl 3,4-diaminobenzoate · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 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 | 382 | 0.78 | 0.87 | 56 | ADN |
| 2 | 399 | 0.77 | 0.87 | 59 | ADN |
| 3 | 591 | 0.70 | 0.79 | 67 | empty |
| 4 | 129 | 0.52 | 0.80 | 22 | DMS |
| 5 | 110 | 0.47 | 0.79 | 16 | DMS |
Interfaces
1 interface between chains.
- A–B · 968 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4K8T · 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 4K8T · PDBe 4K8T · UniProt Q2KDX6
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