Brand  (β version)

color scheme of protein:

hetatm:

x
information
centroid:
interaction residue:

chain: Hide other chain(s)

Ligands
Code Name Link
006 (4r)-3-[(2s,3s)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1s,2r)-2-hydroxy-2,3-dihydro-1h-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide
GOL Glycerol
Code : 3KDB
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10006
Release Data : 2010-03-02
Compound :
mol_id molecule chains synonym
1 Protease A,B Retropepsin, PR
ec: 3.4.23.16
fragment: UNP residues 501-599
mutation: Q7K, L33I, L63I
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1  (taxid:11686) HIV-1 Escherichia coli  (taxid:562)
strain: SUBTYPE B
gene: gag-pol
expression_system_strain: Bl21(de3)
expression_system_vector_type: Plasmid
expression_system_plasmid: pET24a+
Authors : Chufan, E.E., Lafont, V., Freire, E., Amzel, L.M.
Keywords : VIRAL PROTEIN, Hydrolase, Protease, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.66 Å )
Citation :

How much binding affinity can be gained by filling a cavity?

Kawasaki, Y.,Chufan, E.E.,Lafont, V.  et al.
(2010)  Chem.Biol.Drug Des.  75 : 143 - 151

PubMed: 20028396
DOI: 10.1111/j.1747-0285.2009.00921.x

Chain : A, B
UniProt : P03367 (POL_HV1BR)
Reaction : Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).