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(-) Description

Title :  HIV-1 PR RESISTANT MUTANT + LPV
 
Authors :  P. Rezacova, J. Brynda, M. Kozisek, K. Saskova, J. Konvalinka
Date :  16 Oct 07  (Deposition) - 05 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Resistence, Insertion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kozisek, K. G. Saskova, P. Rezacova, J. Brynda, N. M. Van Maarseveen, D. De Jong, C. A. Boucher, R. M. Kagan, M. Nijhuis, J. Konvalinka
Ninety-Nine Is Not Enough: Molecular Characterization Of Inhibitor-Resistant Human Immunodeficiency Virus Type 1 Protease Mutants With Insertions In The Flap Region
J. Virol. V. 82 5869 2008
PubMed-ID: 18400858  |  Reference-DOI: 10.1128/JVI.02325-07

(-) Compounds

Molecule 1 - PROTEASE RETROPEPSIN
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET LIKE, T7 PROMOTOR DRIVEN
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: TYPE B
    Synonym: HIV-1 PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1AB11Ligand/IonN-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , GLY A:49 , GLY A:50 , ILE A:51 , PRO A:82 , HOH A:1005 , HOH A:1064 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , GLY B:49 , GLY B:50 , ILE B:51 , PRO B:82 , HOH B:1006 , HOH B:1010 , HOH B:1063 , HOH B:1064 , HOH B:1077BINDING SITE FOR RESIDUE AB1 B 501
2AC2SOFTWARETRP A:6 , ASP B:29 , ARG B:88 , ASN B:89BINDING SITE FOR RESIDUE GOL B 1001
3AC3SOFTWAREASP A:29 , ARG A:88 , ASN A:89 , TRP B:6BINDING SITE FOR RESIDUE GOL A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RKG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RKG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RKG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RKG)

(-) Exons   (0, 0)

(no "Exon" information available for 2RKG)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:100
 aligned with A0F6C5_9HIV1 | A0F6C5 from UniProtKB/TrEMBL  Length:500

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
         A0F6C5_9HIV1     1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMNLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
               SCOP domains d2rkga_ A: Human immunodeficiency virus type 1 protease                                              SCOP domains
               CATH domains 2rkgA00 A:1-100 Acid Proteases                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeee.......ee..........eeeeee....eeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2rkg A   1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
                                    10        20        30        40        50        60        70        80        90       100


Chain A from PDB  Type:PROTEIN  Length:100
 aligned with A0F7J4_9HIV1 | A0F7J4 from UniProtKB/TrEMBL  Length:499

    Alignment length:100
                                                             34                                                                 
                                                           33 |                                                                 
                                    10        20        30  | |   39        49        59        69        79        89        99
         A0F7J4_9HIV1     1 PQITLWQRPFVTIKIGGQLKEALLDTGADDTIL-EEMNLPGRWTPKIVGGIGGFLKVRQYDQIPVEICGHKVIGTVLVGPTPANIIGRNLLTQLGCTLNF  99
               SCOP domains d2rkga_ A: Human immunodeficiency virus type 1 protease                                              SCOP domains
               CATH domains 2rkgA00 A:1-100 Acid Proteases                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeee.......ee..........eeeeee....eeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2rkg A   1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
                                    10        20        30        40        50        60        70        80        90       100


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with A0F6C5_9HIV1 | A0F6C5 from UniProtKB/TrEMBL  Length:500

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
         A0F6C5_9HIV1     1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMNLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
               SCOP domains d2rkgb_ B: Human immunodeficiency virus type 1 protease                                              SCOP domains
               CATH domains 2rkgB00 B:1-100 Acid Proteases                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeee.......ee..........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2rkg B   1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
                                    10        20        30        40        50        60        70        80        90       100


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with A0F7J4_9HIV1 | A0F7J4 from UniProtKB/TrEMBL  Length:499

    Alignment length:100
                                                             34                                                                 
                                                           33 |                                                                 
                                    10        20        30  | |   39        49        59        69        79        89        99
         A0F7J4_9HIV1     1 PQITLWQRPFVTIKIGGQLKEALLDTGADDTIL-EEMNLPGRWTPKIVGGIGGFLKVRQYDQIPVEICGHKVIGTVLVGPTPANIIGRNLLTQLGCTLNF  99
               SCOP domains d2rkgb_ B: Human immunodeficiency virus type 1 protease                                              SCOP domains
               CATH domains 2rkgB00 B:1-100 Acid Proteases                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeee.......ee..........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2rkg B   1 PQITLWQRPFVTVKIAGQLMEALLDTGADDTILEEEMSLPGRWTPKVVGGIGGFMKVRQYDQILVEICGHKVIGTVLVGPTPANIIGRNLLTQIGCTLNF 100
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RKG)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A0F7J4_9HIV1 | A0F7J4)
molecular function
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain A,B   (A0F6C5_9HIV1 | A0F6C5)
molecular function
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        A0F7J4_9HIV1 | A0F7J4: 2rkf

(-) Related Entries Specified in the PDB File

2rkf