Structure of PDB 3kfn Chain A

Receptor sequence

>3kfnA (length=99) Species: 11676 (Human immunodeficiency virus 1)

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGI
GGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

3D structure

• PDB: 3kfn Fragment-based screen against HIV protease.
• Chain: A
• Resolution: 1.77 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• 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	3TL	A	R8 D25 G27 A28 D29 G48 G49 F53 P81 V82 I84	R8 D25 G27 A28 D29 G48 G49 F53 P81 V82 I84	PDBbind-CN: -logKd/Ki=4.74,IC50=18uM
BS02	4DX	A	K14 I15 G17 L63 I64	K14 I15 G17 L63 I64

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3kfn, PDBe:3kfn, PDBj:3kfn
• PDBsum: 3kfn
• PubMed: 20659109
• UniProt: P12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)