Structure of PDB 3ao2 Chain A

Receptor sequence

>3ao2A (length=138) Species: 11676 (Human immunodeficiency virus 1)

SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTGATVRAACDWAGIKQEESMNKELKKIIGQVRDQA
EHLKTAVQMAVFIHNHKRKGGGYSAGERIVDIIATDIQ

3D structure

• PDB: 3ao2 Fragment-based design of ligands targeting a novel site on the integrase enzyme of human immunodeficiency virus 1
• Chain: A
• Resolution: 1.8 Å

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.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MG	A	D64 C65 D116	D8 C9 D60
BS02	AVX	A	H185 S195 G197 E198 V201	H116 S124 G126 E127 V130	MOAD: Kd=0.17mM PDBbind-CN: -logKd/Ki=3.77,Kd=0.17mM
BS03	AVX	A	G106 R107 W108 P109	G50 R51 W52 P53	MOAD: Kd=0.17mM PDBbind-CN: -logKd/Ki=3.77,Kd=0.17mM

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:3ao2, PDBe:3ao2, PDBj:3ao2
• PDBsum: 3ao2
• PubMed: 21275048
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)