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(-) Description

Title :  CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 PROTEASE IN COMPLEX WITH RITONAVIR
 
Authors :  R. S. Yedidi, H. Garimella, S. B. Chang, J. D. Kaufman, D. Das, P. T. Wingf H. Mitsuya
Date :  11 Nov 13  (Deposition) - 02 Apr 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Multidrug-Resistance, Hiv-1 Protease, Ritonavir, Rit, Protease Inhibitor, Kaletra, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Yedidi, H. Garimella, M. Aoki, H. Aoki-Ogata, D. V. Desai, S. B. Chang, D. A. Davis, W. S. Fyvie, J. D. Kaufman, D. W. Smith, D. Das, P. T. Wingfield, K. Maeda, A. K. Ghosh, H. Mitsuya
A Conserved Hydrogen-Bonding Network Of P2 Bis-Tetrahydrofuran-Containing Hiv-1 Protease Inhibitors (Pis) With A Protease Active-Site Amino Acid Backbone Aids In Their Activity Against Pi-Resistant Hiv.
Antimicrob. Agents Chemother. V. 58 3679 2014
PubMed-ID: 24752271  |  Reference-DOI: 10.1128/AAC.00107-14

(-) Compounds

Molecule 1 - PROTEASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POL
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1RIT2Ligand/IonRITONAVIR
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1RIT1Ligand/IonRITONAVIR
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1RIT1Ligand/IonRITONAVIR

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , VAL A:32 , GLY A:48 , GLY A:49 , ILE A:50 , PRO A:81 , THR A:82 , ILE A:84 , HOH A:603 , HOH A:628 , HOH A:633 , HOH A:666 , ARG B:8 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , GLY B:48 , GLY B:49 , ILE B:50 , PRO B:81 , THR B:82 , ILE B:84 , HOH B:107 , HOH B:164BINDING SITE FOR RESIDUE RIT A 500
2AC2SOFTWAREARG C:8 , ASP C:25 , GLY C:27 , ALA C:28 , ASP C:29 , VAL C:32 , ILE C:47 , GLY C:48 , GLY C:49 , ILE C:50 , PRO C:81 , THR C:82 , ILE C:84 , HOH C:159 , ARG D:8 , ASP D:25 , GLY D:27 , ALA D:28 , ASP D:29 , ASP D:30 , GLY D:48 , GLY D:49 , ILE D:50 , PRO D:81 , THR D:82 , ILE D:84 , HOH D:602 , HOH D:612 , HOH D:654 , HOH D:696BINDING SITE FOR RESIDUE RIT D 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NJV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NJV)

(-) 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
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4njv A  1 PQITLWQRPIVTIKVGGQLKEALLDTGADDTVLEDMELPGRWKPRMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPTPTNIIGRNLMTQLGFTLNF 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
                  4njv B  1 PQITLWQRPIVTIKVGGQLKEALLDTGADDTVLEDMELPGRWKPRMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPTPTNIIGRNLMTQLGFTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain C from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4njv C  1 PQITLWQRPIVTIKVGGQLKEALLDTGADDTVLEDMELPGRWKPRMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPTPTNIIGRNLMTQLGFTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain D 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...eeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4njv D  1 PQITLWQRPIVTIKVGGQLKEALLDTGADDTVLEDMELPGRWKPRMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPTPTNIIGRNLMTQLGFTLNF 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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NJV)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        Q9J006_9HIV1 | Q9J006: 4njs 4njt 4nju 4rvi 4rvj 4rvx

(-) Related Entries Specified in the PDB File

4njs CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 PROTEASE IN COMPLEX WITH NON-PEPTIDIC INHIBITOR, GRL008
4njt CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 PROTEASE IN COMPLEX WITH DARUNAVIR
4nju CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 PROTEASE IN COMPLEX WITH TIPRANAVIR