Structure of PDB 8w2r Chain I

Receptor sequence

>8w2rI (length=258) Species: 11676 (Human immunodeficiency virus 1)

DGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHG
QVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLL
KLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIE
SMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVD
IIATDIQTKELQKQITKIQNFRVYYRGPAKLLWKGEGAVVIQDNSDIKVV
PRRKAKII

3D structure

• PDB: 8w2r HIV-1 integrase assembles multiple species of stable synaptic complex intasomes that are active for concerted DNA integration in vitro.
• Chain: I
• Resolution: 3.23 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	N18 K46	N16 K44
BS02	dna	I	P30 A49 M50 H51	P28 A47 M48 H49
BS03	dna	I	H51 G52 Q53 V54 G140 I141 N144 Q146 S147 G149 S153 M154	H49 G50 Q51 V52 G138 I139 N142 Q144 S145 G147 S151 M152
BS04	dna	I	T66 H67 E152 K156 K159	T64 H65 E150 K154 K157
BS05	MG	I	D64 D116	D62 D114
BS06	MG	I	D64 E152	D62 E150
BS07	ZN	I	H12 H16 C40	H10 H14 C38
BS08	DLU	I	D64 D116 G118 P145 Q146 E152	D62 D114 G116 P143 Q144 E150

Gene Ontology

Molecular Function

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

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:8w2r, PDBe:8w2r, PDBj:8w2r
• PDBsum: 8w2r
• PubMed: 38582148
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)