Research workbench
Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with 1-(4-methoxyphenyl)-1-cyclopropane and 2- aminoperimidine
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
- 4K8K
- Type
- protein
- Length
- 661 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar kinase
- UniProt
- Q2KDX6
- Ligands
- 1PK, ADN, 1PJ, K
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sugar kinase | protein | 331 | 44% helix, 21% strand | Q2KDX6 |
| B | Sugar kinase | protein | 330 | 44% helix, 22% strand | Q2KDX6 |
Ligands and binding sites
- 1PK · 1H-perimidin-2-amine · ligand · 8 copies · chains A, B
- ADN · Adenosine · ligand · 2 copies · chains A, B
- 1PJ · 1-(4-methoxyphenyl)cyclopropanecarboxylic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.77 | 0.86 | 59 | ADN |
| 2 | 397 | 0.77 | 0.86 | 59 | ADN |
| 3 | 196 | 0.62 | 0.83 | 37 | empty |
| 4 | 142 | 0.61 | 0.85 | 26 | empty |
| 5 | 283 | 0.52 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1088 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4K8K · 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 4K8K · PDBe 4K8K · UniProt Q2KDX6
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