Research workbench
1.95 ångström resolution crystal structure of N-acetyl-D-glucosamine kinase from vibrio vulnificus.
Analyse 1.95 ångström resolution crystal structure of N-acetyl-D-glucosamine kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DB3
- Type
- protein
- Length
- 311 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-D-glucosamine kinase
- EC
- 2.7.1.59
- UniProt
- Q8D9M7
- Ligands
- ZN, CL, SO4
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-D-glucosamine kinase (EC 2.7.1.59) | protein | 311 | 41% helix, 21% strand | Q8D9M7 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.47 | 0.75 | 33 | empty |
| 2 | 92 | 0.40 | 0.77 | 18 | empty |
Compared structures
- 4DB3 · 1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8D9M7 · AlphaFold monomer V2.0 prediction for N-acetyl-D-glucosamine kinase (Q8D9M7) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8D9M7
- Elsewhere: RCSB PDB 4DB3 · PDBe 4DB3 · UniProt Q8D9M7
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