Structure of PDB 5i3u Chain C

Receptor sequence

>5i3uC (length=553) Species: 11678 (Human immunodeficiency virus type 1 BH10)

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLP
QGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRET
KLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVS

3D structure

• PDB: 5i3u Conformational States of HIV-1 Reverse Transcriptase for Nucleotide Incorporation vs Pyrophosphorolysis-Binding of Foscarnet.
• Chain: C
• Resolution: 3.0 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	C	W24 R72 L74 R78 N81 E89 I94 A114 Y115 G152 K154 P157 Y183 D185 M230 G231 Q258 K259 G262 K263 W266 S280 R284 K353 H361 R448 T473 Q475 Y501	W24 R72 L74 R78 N81 E89 I94 A114 Y115 G152 K154 P157 Y183 D185 M230 G231 Q258 K259 G262 K263 W266 S280 R284 K353 H361 R448 T473 Q475 Y501
BS02	MG	C	D443 D549	D443 D549

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003964 RNA-directed DNA polymerase activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity

Biological Process

• GO:0006278 RNA-templated DNA biosynthetic process

External links

• PDB: RCSB:5i3u, PDBe:5i3u, PDBj:5i3u
• PDBsum: 5i3u
• PubMed: 27192549
• UniProt: P03366|POL_HV1B1 Gag-Pol polyprotein (Gene Name=gag-pol)