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(-) Description

Title :  HIV-1 PROTEASE TRIPLE MUTANTS V32I, I47V, V82I WITH ANTIVIRAL DRUG SAQUINAVIR
 
Authors :  Y. -F. Tie, Y. -F. Wang, I. T. Weber
Date :  20 May 11  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Saquinavir, Hiv/Aids, Drug Resistance, Aspartic Protease, Molecular Recognition, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tie, Y. F. Wang, P. I. Boross, T. Y. Chiu, A. K. Ghosh, J. Tozser, J. M. Louis, R. W. Harrison, I. T. Weber
Critical Differences In Hiv-1 And Hiv-2 Protease Specificit For Clinical Inhibitors.
Protein Sci. V. 21 339 2012
PubMed-ID: 22238126  |  Reference-DOI: 10.1002/PRO.2019

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POL
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ROC2Ligand/Ion(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ROC2Ligand/Ion(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE

(-) 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:48 , GLY A:49 , ILE A:50 , LYS A:55 , THR A:80 , PRO A:81 , ILE A:82 , HOH A:1045 , HOH A:1052 , ARG B:8 , LEU B:23 , ASP B:25 , GLY B:27 , GLY B:48 , ILE B:50 , ILE B:84 , ROC B:203 , ACT B:501BINDING SITE FOR RESIDUE ROC A 201
2AC2SOFTWAREARG A:8 , PRO A:44 , PRO A:81 , ROC A:201 , ARG B:8 , GLU B:21 , GLU B:34 , PRO B:81 , ILE B:82 , HOH B:1074BINDING SITE FOR RESIDUE ROC B 203
3AC3SOFTWAREROC A:201 , GLY B:27 , ASP B:29 , HOH B:1030BINDING SITE FOR RESIDUE ACT B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S56)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S56)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S56)

(-) Exons   (0, 0)

(no "Exon" information available for 3S56)

(-) Sequences/Alignments

Asymmetric 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 Q7SSI0_9HIV1 | Q7SSI0 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q7SSI0_9HIV1    1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGSTLNF 99
               SCOP domains d3s56a_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3s56 A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTIIEEMSLPGRWKPKMVGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPINIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q7SSI0_9HIV1 | Q7SSI0 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q7SSI0_9HIV1    1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGSTLNF 99
               SCOP domains d3s56b_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- 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
                  3s56 B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTIIEEMSLPGRWKPKMVGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPINIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S56)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7SSI0_9HIV1 | Q7SSI0)
molecular function
    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: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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  3s56
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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
        Q7SSI0_9HIV1 | Q7SSI0: 3ndu 3ndw 3ndx
UniProtKB/TrEMBL
        Q7SSI0_9HIV1 | Q7SSI0: 2avo 2g69 2hb3 2hs1 2hs2 2i4u 2idw 2ieo 2nmy 2nmz 2nnk 2nnp 3b7v 3b80 3oxc 3s53 3s54 4kb9 5e5j 5t8h

(-) Related Entries Specified in the PDB File

2nmy HIV1 PROTEASE MUTANT V82A WITH SAQUINAVIR
2nmz HIV1 PROTEASE MUTANT V82A WITH SAQUINAVIR
3oxc WILD TYPE HIV-1 PROTEASE WITH ANTIVIRAL DRUG SAQUINAVIR
3s43 HIV-1 PROTEASE TRIPLE MUTANTS V32I, I47V, V82I WITH ANTIVIRAL DRUG AMPRENAVIR
3s53 HIV-1 PROTEASE TRIPLE MUTANTS V32I, I47V, V82I WITH ANTIVIRAL DRUG DARUNAVIR IN SPACE GROUP P212121
3s54 HIV-1 PROTEASE TRIPLE MUTANTS V32I, I47V, V82I WITH ANTIVIRAL DRUG DARUNAVIR IN SPACE GROUP P21212