Structure of PDB 3djk Chain B

Receptor sequence

>3djkB (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

3D structure

• PDB: 3djk Flexible cyclic ethers/polyethers as novel P2-ligands for HIV-1 protease inhibitors: design, synthesis, biological evaluation, and protein-ligand X-ray studies
• Chain: B
• Resolution: 1.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D125 T126 G127
• 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	G55	B	D125 G127 A128 D129 D130 G148 G149 I150	D25 G27 A28 D29 D30 G48 G49 I50	MOAD: Ki=26pM PDBbind-CN: -logKd/Ki=10.59,Ki=26pM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3djk, PDBe:3djk, PDBj:3djk
• PDBsum: 3djk
• PubMed: 18783203
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)