Structure of PDB 4bdy Chain A

Receptor sequence

>4bdyA (length=368) Species: 11963 (Human spumaretrovirus)

LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKI
VLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNK
ASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYP
TKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLE
FSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTY
SPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPST
PPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDH
LGNNRTVSIDNLKPTSHQ

3D structure

• PDB: 4bdy Activities, Crystal Structures and Molecular Dynamics of Dihydro-1H-Isoindole Derivatives, Inhibitors of HIV-1 Integrase.
• Chain: A
• Resolution: 2.52 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	A	I112 L113 R114 P115 E207 F208 T210 Q215 S216 G218 K219 R222 R229 S258 K345 N348 R350 T351	I105 L106 R107 P108 E200 F201 T203 Q208 S209 G211 K212 R215 R222 S251 K338 N341 R343 T344
BS02	dna	A	E221 R222 S225 K228 K262	E214 R215 S218 K221 K255
BS03	ZN	A	H62 H66 C96 C99	H55 H59 C89 C92
BS04	MG	A	D128 D185	D121 D178
BS05	MG	A	D128 E221	D121 E214
BS06	CIJ	A	D128 D185 P214 Q215 E221	D121 D178 P207 Q208 E214

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:4bdy, PDBe:4bdy, PDBj:4bdy
• PDBsum: 4bdy
• PubMed: 23075516
• UniProt: P14350|POL_FOAMV Pro-Pol polyprotein (Gene Name=pol)