Structure of PDB 3gp9 Chain D Binding Site BS02

Receptor Information

>3gp9 Chain D (length=131) Species: 212035 (Acanthamoeba polyphaga mimivirus)

GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQH
YKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIR
GDLANDIRENLIHASDSEDSAVDEISIWFPE

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 3gp9 Chain D Residue 139

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gp9 Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): N91 I92 R99
• Binding residue (residue number reindexed from 1): N92 I93 R100
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K9 Y50 N109 H112 E123
• Catalytic site (residue number reindexed from 1): K10 Y51 N110 H113 E124
• Enzyme Commision number: 2.7.4.6: nucleoside-diphosphate kinase.

Gene Ontology

Molecular Function

• GO:0004550 nucleoside diphosphate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006183 GTP biosynthetic process
• GO:0006228 UTP biosynthetic process
• GO:0006241 CTP biosynthetic process
• GO:0009117 nucleotide metabolic process
• GO:0009142 nucleoside triphosphate biosynthetic process
• GO:0016310 phosphorylation

External links

• PDB: RCSB:3gp9, PDBe:3gp9, PDBj:3gp9
• PDBsum: 3gp9
• PubMed: 19439473
• UniProt: Q5UQL3|NDK_MIMIV Nucleoside diphosphate kinase (Gene Name=NDK)