Structure of PDB 3qio Chain A

Receptor sequence

>3qioA (length=136) Species: 11706,83333

MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQ
KTELQAIYLALQDSGLEVNIVTDSQYALGIITQWIHNWKKNVDLVNQIIE
QLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKV

3D structure

• PDB: 3qio Structural and Binding Analysis of Pyrimidinol Carboxylic Acid and N-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors.
• Chain: A
• Resolution: 1.4011 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D443 G444 E478 D498 H539 D549
• Catalytic site (residue number reindexed from 1): D18 G19 E53 D73 H116 D126
• 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.
  3.1.26.4: 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	MN	A	D443 E478 D498	D18 E53 D73
BS02	MN	A	D443 D549	D18 D126
BS03	QID	A	D443 D498 H539 R557	D18 D73 H116 R134	MOAD: Kd=144nM PDBbind-CN: -logKd/Ki=6.84,Kd=144nM

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004523 RNA-DNA hybrid ribonuclease activity

External links

• PDB: RCSB:3qio, PDBe:3qio, PDBj:3qio
• PDBsum: 3qio
• PubMed: 21464257
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol);
  P0A7Y4|RNH_ECOLI Ribonuclease HI (Gene Name=rnhA)