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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF HIV-1 PROTEASE VARIANT G48T/L89M IN COMPLEX WITH SAQUINAVIR
 
Authors :  B. P. Mahon, R. Mckenna, N. Goldfarb
Date :  22 May 14  (Deposition) - 16 Jul 14  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Saquinavir, Hiv Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. E. Goldfarb, M. Ohanessian, S. Biswas, T. D. Mcgee, B. P. Mahon, D. A. Ostrov, J. Garcia, Y. Tang, R. Mckenna, A. Roitberg, B. M. Dunn
Defective Hydrophobic Sliding Mechanism And Active Site Expansion In Hiv-1 Protease Drug Resistant Variant Gly48Thr/Leu89Met: Mechanisms For The Loss Of Saquinavir Binding Potency.
Biochemistry V. 54 422 2015
PubMed-ID: 25513833  |  Reference-DOI: 10.1021/BI501088E

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 STAR DE3 PLYSS
    Expression System Taxid: 511693
    Expression System Vector Type: PJEXPRESS
    Fragment: HIV-1 PROTEASE CHAIN A, UNP RESIDUES 489-587
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 LW12.3 ISOLATE
    Organism Taxid: 82834
    Synonym: GAG-POL POLYPROTEIN, PR RETROPEPSIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ROC1Ligand/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  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , THR A:48 , GLY A:49 , ILE A:50 , HOH A:201 , HOH A:218 , ARG B:8 , LEU B:23 , ASP B:25 , THR B:48 , GLY B:49 , ILE B:50 , PRO B:81 , ILE B:84BINDING SITE FOR RESIDUE ROC A 101
2AC2SOFTWAREILE A:54 , PRO A:79 , TRP B:42 , ILE B:50 , HOH B:152BINDING SITE FOR RESIDUE GOL A 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QGI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QGI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QGI)

(-) Exons   (0, 0)

(no "Exon" information available for 4QGI)

(-) 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
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4qgi A  1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMITGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNMLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4qgi B  1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMITGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNMLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QGI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QGI)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        POL_HV1LW | P0C6F2: 3lp3 3th9 3vfa 4i8w 4i8z 4mc1 4mc2 4mc6 4mc9 4nyf 5k14

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