Structure of PDB 3oyd Chain A Binding Site BS04

Receptor Information

>3oyd Chain A (length=368) Species: 11963 (Human spumaretrovirus)

LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNK
ASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYP
TKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLE
FSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTY
SPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPST
PPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQ

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: 3oyd Chain A Residue 396

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3oyd Molecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance.
• Resolution: 2.54 Å
• Binding residue (original residue number in PDB): D128 D185
• Binding residue (residue number reindexed from 1): D121 D178
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.26.4: ribonuclease H.
  3.4.23.-

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:3oyd, PDBe:3oyd, PDBj:3oyd
• PDBsum: 3oyd
• PubMed: 21030679
• UniProt: P14350|POL_FOAMV Pro-Pol polyprotein (Gene Name=pol)