Structure of PDB 3gp9 Chain E Binding Site BS03

Receptor Information

>3gp9 Chain E (length=132) Species: 212035 (Acanthamoeba polyphaga mimivirus)

GLQRTLVLIKPDAFERSLVAEIMGRIEKKNFKIVSMKFWSKAPRNLIEQH
YKEHSEQSYFNDNCDFMVSGPIISIVYEGTDAISKIRRLQGNILTPGTIR
GDLANDIRENLIHASDSEDSAVDEISIWFPET

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 3gp9 Chain E Residue 140

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): R86 Q89 H112 A113
• Binding residue (residue number reindexed from 1): R87 Q90 H113 A114
• 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)