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(-) Description

Title :  DARUNAVIR IN COMPLEX WITH A HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE VARIANT
 
Authors :  Y. Wang, Z. Liu, S. J. Brunzelle, L. C. Kovari, I. A. Kovari
Date :  30 Jun 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.87
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multi-Drug Resistance, Hiv-1 Protease, Darunavir, Protease Inhibitor, Hydorlase-Hydorlase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, Z. Liu, J. S. Brunzelle, I. A. Kovari, T. G. Dewdney, S. J. Reiter, L. C. Kovari
The Higher Barrier Of Darunavir And Tipranavir Resistance For Hiv-1 Protease.
Biochem. Biophys. Res. Commun. V. 412 737 2011
PubMed-ID: 21871444  |  Reference-DOI: 10.1016/J.BBRC.2011.08.045

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HIV-1 PROTEASE, UNP RESIDUES 1-99
    Gene: POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: THE SEQUENCE IS A CLINICAL ISOLATE WITH MUTATIONS INTRODUCED.
    Strain: MDR769

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
10171Ligand/Ion(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , GLY A:48 , GLY A:49 , ILE A:50 , HOH A:173 , ASN B:25 , ALA B:28 , ASP B:29 , ASP B:30 , GLY B:48 , GLY B:49 , ILE B:50 , THR B:82BINDING SITE FOR RESIDUE 017 A 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SO9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SO9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SO9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SO9)

(-) Exons   (0, 0)

(no "Exon" information available for 3SO9)

(-) 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:99
 aligned with Q000H7_9HIV1 | Q000H7 from UniProtKB/TrEMBL  Length:404

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q000H7_9HIV1    1 PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEDINLPGRWKPKMIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPTNVIGRNLMTQIGCTLNF 99
               SCOP domains d3so9a_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeee......eee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3so9 A  1 PQITLWKRPIVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPTNVIGRNLMTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q000H7_9HIV1 | Q000H7 from UniProtKB/TrEMBL  Length:404

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q000H7_9HIV1    1 PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEDINLPGRWKPKMIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPTNVIGRNLMTQIGCTLNF 99
               SCOP domains d3so9b_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eee........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3so9 B  1 PQITLWKRPIVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPTNVIGRNLMTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90
   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  (0, 0)

(no "CATH Domain" information available for 3SO9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SO9)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q000H7_9HIV1 | Q000H7)
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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  3.4.23.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q000H7_9HIV1 | Q000H7: 3oq7 3oqa 3oqd 3oty 3ou1 3ou3 3ou4 3oua 3oub 3ouc 3oud 3pj6
UniProtKB/TrEMBL
        Q000H7_9HIV1 | Q000H7: 3r0w 3r0y 3spk 4eyr 4fae 4faf 4l1a 4nkk

(-) Related Entries Specified in the PDB File

1rpi UNCOMPLEXED HIV-1 PROTEASE VARIANT, MDR 769
1tw7 UNCOMPLEXED HIV-1 PROTEASE VARIANT, MDR 769
3oq7 UNCOMPLEXED HIV-1 PROTEASE VARIANT, MDR 769 82T
3oqa SAME PROTEIN WITH MUTATION A82S
3oqd SAME PROTEIN WITH MUTATION A82F
3spk SAME PROTEIN COMPLEX WITH TIPRANAVIR