MolNFT v1 · #97290 · protein
Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE and 4-methyl-3,4- dihydro-2H-1,4-benzoxazine-7-carboxylic acid
4K9C: “Crystal structure of probable sugar kinase protein from rhizobium etli cfn 42 complexed with…”. X-ray diffraction, 4 ligands (ADN, C29, 1Q8), 5 pockets (best druggability 0.78). MolNFT v1 #97290 on GenesisL1: 3D structure, binding…
- PDB
- 4K9C
- 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, C29, 1Q8, 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
- C29 · 4-methyl-3,4-dihydro-2H-1,4-benzoxazine-7-carboxylic acid · ligand · 2 copies · chains A, B
- 1Q8 · N-(hydroxymethyl)benzamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.78 | 0.87 | 59 | ADN |
| 2 | 394 | 0.77 | 0.86 | 59 | ADN |
| 3 | 617 | 0.72 | 0.80 | 65 | empty |
| 4 | 126 | 0.48 | 0.78 | 19 | DMS, 1Q8 |
| 5 | 118 | 0.48 | 0.79 | 16 | DMS, 1Q8 |
Interfaces
1 interface between chains.
- A–B · 937 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 4K9C · 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 4K9C · PDBe 4K9C · UniProt Q2KDX6
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