Structure of PDB 3lp1 Chain A

Receptor sequence

>3lp1A (length=554) Species: 11706 (HIV-1 M:B_HXB2R)

SPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISK
IGPENPYNTPVFAIKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKN
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
AGIR

3D structure

• PDB: 3lp1 Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors.
• Chain: A
• Resolution: 2.23 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	LP8	A	D443 E478 D498 H539	D440 E475 D495 H536	PDBbind-CN: -logKd/Ki=6.92,IC50=0.12uM
BS02	MN	A	D443 D549	D440 D546
BS03	MN	A	D443 E478 D498	D440 E475 D495

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003964 RNA-directed DNA polymerase activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity

Biological Process

• GO:0006278 RNA-templated DNA biosynthetic process

External links

• PDB: RCSB:3lp1, PDBe:3lp1, PDBj:3lp1
• PDBsum: 3lp1
• PubMed: 20484498
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)