Structure of PDB 4db3 Chain A Binding Site BS01

Receptor Information

>4db3 Chain A (length=311) Species: 672 (Vibrio vulnificus)

NLYFQSNAMYYGFDVGGTKIEFGAFNEKLERVATERVPTPTDDYPLLLET
IAGLVAKYDQEFACEGKIGLGLPGMEDADDATVLTVNVPAAKGKPLRADL
EAKIGRSVKIENDANCFALSEAWDEELQDAPSVMGLILGTGFGGGLIYEG
KVFSGRNNVAGELGHMRLPLDAWFHLGDNAPLLGCGCGKKGCLDSYLSGR
GFELLYAHYYGEEKKAIDIIKANAAGDEKAAEHVERFMELLAICFGNIFT
ANDPHVVALGGGLSNFELIYEEMPKRVPKYLLSVAKCPKIIKAKHGDSGG
VRGAAFLNIKG

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 4db3 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4db3 1.95 Angstrom Resolution Crystal Structure of N-acetyl-D-glucosamine kinase from Vibrio vulnificus.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): H157 C177 C179 C184
• Binding residue (residue number reindexed from 1): H165 C185 C187 C192
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.1.59: N-acetylglucosamine kinase.

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0008270 zinc ion binding
• GO:0016301 kinase activity
• GO:0045127 N-acetylglucosamine kinase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006044 N-acetylglucosamine metabolic process
• GO:0009254 peptidoglycan turnover
• GO:0016310 phosphorylation
• GO:0046835 carbohydrate phosphorylation

External links

• PDB: RCSB:4db3, PDBe:4db3, PDBj:4db3
• PDBsum: 4db3
• UniProt: Q8D9M7|NAGK_VIBVU N-acetyl-D-glucosamine kinase (Gene Name=nagK)