Brand  (β version)

PDB ID: 3VF7

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Ligands
Code Name Style Show Link
031 (3as,5r,6ar)-hexahydro-2h-cyclopenta[B]furan-5-yl [(1s,2r)-1-benzyl-2-hydroxy-3-([(4-methoxyphenyl)sulfonyl]{[(2r)-5-oxopyrrolidin-2-yl]methyl}amino)propyl]carbamate PoSSuM
CL Chloride ion PoSSuM
GOL Glycerol PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 3VF7   PDBj   RCSB PDB   PDBe
Header : hydrolase/hydrolase inhibitor
Title : Crystal Structure of HIV-1 Protease Mutant L76V with novel P1'-Ligands GRL-02031
Release Data : 2012-11-21
Compound :
mol_id molecule chains
1 protease A,B
ec: 3.4.23.16
fragment: UNP residues 501-599
mutation: Q507K, L533I, L563I, C567A, L576V, C595A
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1 (BRU ISOLATE)  (taxid:11686) HIV-1 Escherichia coli  (taxid:469008)
gene: gag-pol
expression_system_strain: Bl21 (de3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET11a
Authors : Yu, X.X., Wang, Y.F., Chang, Y.C.E., Weber, I.T.
Keywords : protease inhibitor, P1'-ligand, hydrolase-hydrolase inhibitor complex
Exp. method : X-RAY DIFFRACTION ( 1.30 Å )
Citation :

Potent antiviral HIV-1 protease inhibitor GRL-02031 adapts to the structures of drug resistant mutants with its P1'-pyrrolidinone ring.

Chang, Y.C.,Yu, X.,Zhang, Y.  et al.
(2012)  J.Med.Chem.  55 : 3387 - 3397

PubMed: 22401672
DOI: 10.1021/jm300072d

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
-
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
-
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.