Structure of PDB 5u1c Chain C Binding Site BS07

Receptor Information

>5u1c Chain C (length=251) Species: 2287 (Saccharolobus solfataricus)

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IQSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKII
R

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: 5u1c Chain C Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5u1c Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): D64 D116
• Binding residue (residue number reindexed from 1): D64 D116
• 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.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0004521 RNA endonuclease activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:5u1c, PDBe:5u1c, PDBj:5u1c
• PDBsum: 5u1c
• PubMed: 28059769
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)