Structure of PDB 8dxm Chain A

Receptor sequence

>8dxmA (length=556) Species: 11678 (Human immunodeficiency virus type 1 BH10)

MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKIS
KIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPA
GLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNV
LPQGWKGSPAIFQSSMTKILEPFAAQNPDIVIYQYMDDLYVGSDLEIGQH
RTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPE
KDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEE
AELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKN
LKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETW
ETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANR
ETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTD
SQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQV
DKLVSA

3D structure

• PDB: 8dxm Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening.
• Chain: A
• Resolution: 1.99 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	BML	A	I5 A114 V118 F160 S163 M164 I167 W212 L214	I7 A116 V120 F162 S165 M166 I169 W214 L216
BS02	T27	A	L100 K101 K103 Y181 Y188 F227 W229 L234 H235 P236 Y318	L102 K103 K105 Y183 Y190 F229 W231 L236 H237 P238 Y320
BS03	MG	A	D443 D549	D445 D551

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:8dxm, PDBe:8dxm, PDBj:8dxm
• PDBsum: 8dxm
• PubMed: 37115705
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)