Structure of PDB 5ejk Chain E

Receptor sequence

>5ejkE (length=269) Species: 11888 (Rous sarcoma virus - Prague C)

PLREAKDLHTALHIGPRALSKASNISMQQAREVVQTCPHCNSAPALEAGV
NPRGLGPLQIWQTDFTLEPRMAPRSWLAVTVDTASSAIVVTQHGRVTSVA
VQHHWATAIAVMGRPKAIKTDNGSCFTSKSTREWMARWGIAHTTGIPGNS
QGQAMVERANRMMKDKIRVLAEGDGFMKRIPTSKQGEMMAKAMYALNHFE
RGENTKTPIQKHWRPTVLTEGPPVKIRIETGEWEKGWNVLVWGRGYAAVK
NRDTDKVIWVPSRKVKPDI

3D structure

• PDB: 5ejk Crystal structure of the Rous sarcoma virus intasome.
• Chain: E
• Resolution: 3.8 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.-.-
  3.1.26.4: 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	E	T66 W76 S150 E157 K164	T66 W76 S150 E157 K164
BS02	dna	E	G49 V50 N51 K119 T143 T144 G145 I146 Q151 G152 A154 M155 R158 R161 R201 G202 E203 R244 Y246	G49 V50 N51 K119 T143 T144 G145 I146 Q151 G152 A154 M155 R158 R161 R201 G202 E203 R244 Y246
BS03	dna	E	S26 Q28 E47 R95 V96 T97 S124 S128 K129	S26 Q28 E47 R95 V96 T97 S124 S128 K129
BS04	dna	E	D121 N122 G123 G148	D121 N122 G123 G148
BS05	ZN	E	H9 H13 C37 C40	H9 H13 C37 C40

Gene Ontology

Molecular Function

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

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:5ejk, PDBe:5ejk, PDBj:5ejk
• PDBsum: 5ejk
• PubMed: 26887497
• UniProt: P03354|POL_RSVP Gag-Pol polyprotein (Gene Name=gag-pol)