Structure of PDB 6dbz Chain B Binding Site BS02

Receptor Information

>6dbz Chain B (length=138) Species: 3702 (Arabidopsis thaliana)

AIPRVAVVVFILNGNSILLGRRRSSIGNSTFALPGGHLEFGESFEECAAR
EVMEETGLKIEKMKLLTVTNNVFKEAPTPSHYVSVSIRAVLVDPSQEPKN
MEPEKCEGWDWYDWENLPKPLFWPLEKLFGSGFNPFTH

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: 6dbz Chain B Residue 204

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dbz Contribution of isopentenyl phosphate to plant terpenoid metabolism.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): E56 E60
• Binding residue (residue number reindexed from 1): E51 E55
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.1.22: NAD(+) diphosphatase.
  3.6.1.55: 8-oxo-dGTP diphosphatase.
  3.6.1.67: dihydroneopterin triphosphate diphosphatase.

Gene Ontology

Molecular Function

• GO:0000210 NAD+ diphosphatase activity
• GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
• GO:0016787 hydrolase activity
• GO:0019177 dihydroneopterin triphosphate pyrophosphohydrolase activity
• GO:0035529 NADH pyrophosphatase activity
• GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006974 DNA damage response

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:6dbz, PDBe:6dbz, PDBj:6dbz
• PDBsum: 6dbz
• PubMed: 30127411
• UniProt: Q9CA40|NUDT1_ARATH Nudix hydrolase 1 (Gene Name=NUDT1)