Structure of PDB 8fnd Chain A

Receptor sequence

>8fndA (length=261) Species: 9606,11698

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQKFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYRKGPAKLLWKGEGAVVIQDNSDI
KVVPRRKAKII

3D structure

• PDB: 8fnd Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants.
• Chain: A
• Resolution: 3.0 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	H51 G52 Q53 V54 G140 I141 N144 Q146 S147 G149 V150 S153	H51 G52 Q53 V54 G140 I141 N144 Q146 S147 G149 V150 S153
BS02	dna	A	T66 E152 K156 K159	T66 E152 K156 K159
BS03	dna	A	P30 A49 M50 H51	P30 A49 M50 H51
BS04	MG	A	D64 D116	D64 D116
BS05	MG	A	D64 E152	D64 E152
BS06	ZN	A	H12 H16 C40 C43	H12 H16 C40 C43
BS07	DLU	A	D64 D116 G118 Y143 P145 Q146 E152	D64 D116 G118 Y143 P145 Q146 E152

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:8fnd, PDBe:8fnd, PDBj:8fnd
• PDBsum: 8fnd
• PubMed: 37478179
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol);
  P42166