MolNFT v1 · #97296 · protein
Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with norharmane
4K9I: “Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with norharmane”. X-ray diffraction, 3 ligands (ADN, NRH, K), 5 pockets (best druggability 0.77). MolNFT v1 #97296 on GenesisL1: 3D structure…
- PDB
- 4K9I
- 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, NRH, K
- Pockets
- 5 · best druggability 0.77
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
- NRH · Norharmane · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 6 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 | 398 | 0.77 | 0.86 | 62 | ADN |
| 2 | 414 | 0.77 | 0.86 | 60 | ADN |
| 3 | 665 | 0.72 | 0.79 | 68 | DMS |
| 4 | 90 | 0.53 | 0.84 | 11 | DMS |
| 5 | 120 | 0.49 | 0.80 | 19 | DMS |
Interfaces
1 interface between chains.
- A–B · 925 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4K9I · 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 4K9I · PDBe 4K9I · UniProt Q2KDX6
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