Structure of PDB 6puy Chain A

Receptor sequence

>6puyA (length=261) Species: 11698,273057

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYRKGPAKLLWKGEGAVVIQDNSDI
KVVPRRKAKII

3D structure

• PDB: 6puy Structural basis for strand-transfer inhibitor binding to HIV intasomes.
• Chain: A
• Resolution: 2.8 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 Q146 S147 G149 V150 S153 M154 K156 E157	H51 G52 Q53 V54 G140 I141 Q146 S147 G149 V150 S153 M154 K156 E157
BS02	dna	A	T66 E152 K156	T66 E152 K156
BS03	MG	A	D64 D116	D64 D116
BS04	MG	A	D64 E152	D64 E152
BS05	ZN	A	H12 H16 C40 C43	H12 H16 C40 C43
BS06	OZ1	A	D64 D116 N117 Y143 P145 Q146 E152	D64 D116 N117 Y143 P145 Q146 E152

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0004521 RNA endonuclease activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0015074 DNA integration

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6puy, PDBe:6puy, PDBj:6puy
• PDBsum: 6puy
• PubMed: 32001521
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol);
  P39476|DN7D_SACS2 DNA-binding protein 7d (Gene Name=sso7d)