Structure of PDB 5y5p Chain D Binding Site BS02

Receptor Information

>5y5p Chain D (length=171) Species: 654913 (Shrimp white spot syndrome virus (isolate Tongan))

MDSSASVVFMRFAPPGEETALPPRRATPGSVAYDLFPSEEMDIEPMGLAK
ISTGYGIDKFPDGCYGQIVSRSGMTWKNNTSVPTGTIDVDYRGELKVILR
NHSAEKSVPIRKGTSIAQLIFLRYCDVEEEQIVYINETTGERTIIDSSSK
KDNKNQARSVRGTGGFGSTDN

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 5y5p Chain D Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5y5p The dUTPase of white spot syndrome virus assembles its active sites in a noncanonical manner.
• Resolution: 2.03 Å
• Binding residue (original residue number in PDB): R161 G165 G167 S168 T169
• Binding residue (residue number reindexed from 1): R161 G165 G167 S168 T169
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.1.23: dUTP diphosphatase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004170 dUTP diphosphatase activity

Biological Process

• GO:0006226 dUMP biosynthetic process
• GO:0046081 dUTP catabolic process

External links

• PDB: RCSB:5y5p, PDBe:5y5p, PDBj:5y5p
• PDBsum: 5y5p
• PubMed: 29187596
• UniProt: Q77J78