Structure of PDB 8w09 Chain I

Receptor sequence

>8w09I (length=260) Species: 11676 (Human immunodeficiency virus 1)

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYRGPAKLLWKGEGAVVIQDNSDIK
VVPRRKAKII

3D structure

• PDB: 8w09 HIV-1 integrase assembles multiple species of stable synaptic complex intasomes that are active for concerted DNA integration in vitro.
• Chain: I
• Resolution: 3.2 Å

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	I	K46 G47	K46 G47
BS02	dna	I	A49 M50 H51	A49 M50 H51
BS03	dna	I	H51 G52 Q53 V54 G140 I141 Q146 S147 G149 S153 M154 E157	H51 G52 Q53 V54 G140 I141 Q146 S147 G149 S153 M154 E157
BS04	dna	I	T66 E152 S153 K156 K159	T66 E152 S153 K156 K159
BS05	MG	I	D64 D116	D64 D116
BS06	MG	I	D64 E152	D64 E152
BS07	ZN	I	H12 H16 C40 C43	H12 H16 C40 C43
BS08	DLU	I	D64 D116 P145 E152	D64 D116 P145 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:8w09, PDBe:8w09, PDBj:8w09
• PDBsum: 8w09
• PubMed: 38582148
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)