MolNFT v1 · #97268 · protein
Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with 2-ethylbenzyl alcohol
4K8P: “Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with 2-ethylbenzyl…”. X-ray diffraction, 3 ligands (ADN, 12M, K), 6 pockets (best druggability 0.77). MolNFT v1 #97268 on GenesisL1: 3D…
- PDB
- 4K8P
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sugar kinase
- UniProt
- Q2KDX6
- Ligands
- ADN, 12M, K
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sugar kinase | protein | 332 | 44% helix, 21% strand | Q2KDX6 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- 12M · (2-ethylphenyl)methanol · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.77 | 0.86 | 57 | ADN |
| 2 | 421 | 0.77 | 0.86 | 57 | ADN |
| 3 | 284 | 0.64 | 0.81 | 43 | empty |
| 4 | 355 | 0.62 | 0.78 | 39 | empty |
| 5 | 112 | 0.45 | 0.78 | 14 | 12M, DMS |
Interfaces
1 interface between chains.
- A–B · 955 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4K8P · 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 4K8P · PDBe 4K8P · UniProt Q2KDX6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.