Structure of PDB 5m0r Chain I

Receptor sequence

>5m0rI (length=276) Species: 36374 (Visna/maedi virus EV1 KV1772)

WIENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPS
TLRGSNKRGIDHWQVDYTHYEDKIILVWVETNSGLIYAERVKGETGQEFR
VQTMKWYAMFAPKSLQSDNGPAFVAESTQLLMKYLGIEHTTGIPWNPQSQ
ALVERTHQTLKNTLEKLIPMFNAFESALAGTLITLNIKRKGGLGTSPMDI
FIFNKEQQRIQQQSKSKQEKIRFCYYRTRKRGHPGEWQGPTQVLWGGDGA
IVVKDRGTDRYLVIANKDVKFIPPPK

3D structure

• PDB: 5m0r A supramolecular assembly mediates lentiviral DNA integration.
• Chain: I
• Resolution: 8.2 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.
  3.1.26.4: ribonuclease H.
  3.4.23.-
  3.6.1.23: dUTP diphosphatase.

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	R53 G54 S55 T141 I143 N146 Q148 S149 A151 R155	R53 G54 S55 T141 I143 N146 Q148 S149 A151 R155
BS02	dna	I	H69 P147 Q148 E154 R155 H157 Q158	H69 P147 Q148 E154 R155 H157 Q158
BS03	dna	I	K47 M48 S50 R231 H233	K47 M48 S50 R231 H233
BS04	dna	I	R30 T51 L52 G93 E94 T95 G96 P121 A122 V124 A125 E126	R30 T51 L52 G93 E94 T95 G96 P121 A122 V124 A125 E126
BS05	dna	I	D66 Y67 H69 D118 N119 G120 P121 P144	D66 Y67 H69 D118 N119 G120 P121 P144

Gene Ontology

Molecular Function

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

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:5m0r, PDBe:5m0r, PDBj:5m0r
• PDBsum: 5m0r
• PubMed: 28059770
• UniProt: P35956|POL_VILVK Gag-Pol polyprotein (Gene Name=pol)