Brand  (β version)

PDB ID: 2PK5

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Ligands
Code Name Style Show Link
075 (4r)-N-[(1s,2r)-2-hydroxy-2,3-dihydro-1h-inden-1-yl]-3-[(2s,3s)-2-hydroxy-3-({N-[(isoquinolin-5-yloxy)acetyl]-3-(methyl sulfonyl)-L-alanyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide PoSSuM
GOL Glycerol PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 2PK5   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I ) in Complex with KNI-10075
Release Data : 2007-05-08
Compound :
mol_id molecule chains
1 Protease A,B
mutation: Q7K
Source :
mol_id organism_scientific expression_system
1 Human immunodeficiency virus 1  (taxid:11676) Escherichia coli BL21(DE3)  (taxid:469008)
strain: SUBTYPE B
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: Plasmid
expression_system_plasmid: pET24a+
Authors : Armstrong, A.A., Lafont, V., Kiso, Y., Freire, E., Amzel, L.M.
Keywords : PROTEASE COMPLEX, Viral Protein, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.900 Å )
Citation :

Compensating enthalpic and entropic changes hinder binding affinity optimization.

Lafont, V.,Armstrong, A.A.,Ohtaka, H.  et al.
(2007)  Chem.Biol.Drug Des.  69 : 413 - 422

PubMed: 17581235
DOI: 10.1111/j.1747-0285.2007.00519.x

Reaction

Chain : A, B
UniProt : P03367 (POL_HV1BR)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
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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. 3.1.26.13 -
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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 -
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.49 PROSITE-ProRule:PRU00405
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 PROSITE-ProRule:PRU00405
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Cofactor: Evidence: Note:
Mg(2+) ECO:0000250
Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Mg(2+) ECO:0000250
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.
Mg(2+) ECO:0000250
Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.