Structure of PDB 6wph Chain A Binding Site BS01

Receptor Information

>6wph Chain A (length=548) Species: 11706 (HIV-1 M:B_HXB2R)

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPIRYQYNVLPQGWKGSPA
IFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQH
LLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIC
KLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENRE
ILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMR
GAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQA
TWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYV
TNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQA
QPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGI

Ligand information

>6wph Chain P (length=18)

gtccctgttcgggcgccg

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6wph Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance.
• Resolution: 2.72 Å
• Binding residue (original residue number in PDB): Y183 M230 G231 C258 K259 G262 K263 W266 L289 G359 R448 T473 Q475 K476 Y501
• Binding residue (residue number reindexed from 1): Y175 M222 G223 C250 K251 G254 K255 W258 L281 G351 R440 T465 Q467 K468 Y493

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.

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:6wph, PDBe:6wph, PDBj:6wph
• PDBsum: 6wph
• PubMed: 33096918
• UniProt: P04585|POL_HV1H2 Gag-Pol polyprotein (Gene Name=gag-pol)