Structure of PDB 1jkh Chain A

Receptor sequence

>1jkhA (length=551) Species: 11706 (HIV-1 M:B_HXB2R)

ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLK
KKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETIRYQYNVLPQGW
KGSPAIFQSSMTKILEPFRKQNPDIVICQYMDDLYVGSDLEIGQHRTKIE
ELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWT
VNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELEL
AENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGK
YARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWT
EYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLG
KAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYAL
GIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVS
A

3D structure

• PDB: 1jkh Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors.
• Chain: A
• Resolution: 2.5 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	EFZ	A	L100 K101 V106 C181 Y188 G190 W229 L234 H235 Y318	L99 K100 V105 C178 Y185 G187 W226 L231 H232 Y315	BindingDB: IC50=25nM,Ki=30nM

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:1jkh, PDBe:1jkh, PDBj:1jkh
• PDBsum: 1jkh
• PubMed: 11575933
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)