Structure of PDB 6rny Chain O

Receptor sequence

>6rnyO (length=338) Species: 11963 (Human spumaretrovirus)

KVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRK
DVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQ
GYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQG
AAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVG
RPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLT
REEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRW
HKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ

3D structure

• PDB: 6rny Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer.
• Chain: O
• Resolution: 3.9 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.-.-
  3.1.26.4: ribonuclease H.
  3.4.23.-

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	O	D128 Q137 G138 P214 E221 R222 S225 K262	D91 Q100 G101 P177 E184 R185 S188 K225
BS02	dna	O	D185 Q186 Y212 R329	D148 Q149 Y175 R292
BS03	dna	O	R86 S105 N106 A108 P161 S162 A188 S192 S193 S311 S312 R313 R326 R329 R336	R49 S68 N69 A71 P124 S125 A151 S155 S156 S274 S275 R276 R289 R292 R299
BS04	dna	O	I112 L113 R114 S216 G218 K219 R222 S258 P259 N348 T351	I75 L76 R77 S179 G181 K182 R185 S221 P222 N311 T314
BS05	dna	O	R69 N106 K107 H374	R32 N69 K70 H337
BS06	MG	O	D128 D185	D91 D148

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:6rny, PDBe:6rny, PDBj:6rny
• PDBsum: 6rny
• PubMed: 31519882
• UniProt: P14350|POL_FOAMV Pro-Pol polyprotein (Gene Name=pol)