Structure of PDB 6x4b Chain A

Receptor sequence

>6x4bA (length=549) Species: 11678 (Human immunodeficiency virus type 1 BH10)

ISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIG
PENPYNTPVFAIKKKTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKK
KSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNGIRYQYNVLPQGWKGS
PAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELR
QHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVND
IQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAEN
REILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYAR
MRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYW
QATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAG
YVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGII
QAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG

3D structure

• PDB: 6x4b Structural investigation of 2-naphthyl phenyl ether inhibitors bound to WT and Y181C reverse transcriptase highlights key features of the NNRTI binding site.
• 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	UMY	A	L100 K101 K102 K103 V106 V108 V179 Y181 Y188 V189 G190 W229 L234 H235 P236 Y318	L97 K98 K99 K100 V103 V105 V173 Y175 Y182 V183 G184 W223 L228 H229 P230 Y312
BS02	MG	A	D443 E478 D498	D437 E472 D492

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:6x4b, PDBe:6x4b, PDBj:6x4b
• PDBsum: 6x4b
• PubMed: 32643196
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)