Structure of PDB 6bsj Chain A

Receptor sequence

>6bsjA (length=543) Species: 11676 (Human immunodeficiency virus 1)

PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPE
NPYNTPVFKLVDFRELNKKTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDA
YFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSM
TKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGL
TTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKL
NWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPV
HGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTND
VKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWVPEW
EFVNTPPLVKLWYQLEKEPIVGAETFYVDGAASRETKLGKAGYVTNKGRQ
KVVTLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQYALGIIQAQPDQSE
SELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIR

3D structure

• PDB: 6bsj Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid.
• Chain: A
• Resolution: 2.89 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	dna	A	Q151 M184 M230 G231 N255 Q258 K259 G262 K263 W266 A360 R448	Q137 M170 M216 G217 N241 Q244 K245 G248 K249 W252 A346 R434
BS02	rna	A	K22 W24 P59 R78 N265 C280 L283 R284 G285 N474	K19 W21 P56 R64 N251 C266 L269 R270 G271 N460
BS03	EFZ	A	L100 K101 V106 Y181 Y188 G190 W229 H235	L86 K87 V92 Y167 Y174 G176 W215 H221	BindingDB: IC50=25nM,Ki=30nM
BS04	CA	A	D443 E478 D498	D429 E464 D484

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:6bsj, PDBe:6bsj, PDBj:6bsj
• PDBsum: 6bsj
• PubMed: 29295939
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)