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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH GRL-10413
 
Authors :  R. S. Yedidi, N. S. Delino, D. Das, J. D. Kaufman, P. T. Wingfield, A. K. Gh H. Mitsuya
Date :  01 Jun 16  (Deposition) - 31 Aug 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Grl-10413, Hiv-1 Protease, Protease-Inhibitor, Darunavir, 2- Chloroanisole, Nonpeptidic, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Amano, P. M. Salcedo-Gomez, R. Zhao, R. S. Yedidi, D. Das, H. Bulut, N. S. Delino, V. R. Sheri, A. K. Ghosh, H. Mitsuya
A Modified P1 Moiety Enhances In Vitro Antiviral Activity Against Various Multidrug-Resistant Hiv-1 Variants And In Vitro Central Nervous System Penetration Properties Of A Novel Nonpeptidic Protease Inhibitor, Grl-10413.
Antimicrob. Agents Chemother. V. 60 7046 2016
PubMed-ID: 27620483  |  Reference-DOI: 10.1128/AAC.01428-16

(-) Compounds

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

 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
1G431Ligand/Ion[(3~{A}~{S},4~{R},6~{A}~{R})-2,3,3~{A},4,5,6~{A}-HEXAHYDROFURO[2,3-B]FURAN-4-YL] ~{N}-[(2~{S},3~{R})-1-(3-CHLORANYL-4-METHOXY-PHENYL)-4-[(4-METHOXYPHENYL)SULFONYL-(2-METHYLPROPYL)AMINO]-3-OXIDANYL-BUTAN-2-YL]CARBAMATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
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 , VAL A:82 , HOH A:618 , ARG B:8 , LEU B:23 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , GLY B:48 , GLY B:49 , PRO B:81 , VAL B:82 , ILE B:84binding site for residue G43 A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KAO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KAO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5KAO)

(-) 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    
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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........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  5kao A  1 PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF 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......eeee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee....eeehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  5kao B  1 PQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90
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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 5KAO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KAO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KAO)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q72874_9HIV1 | Q72874: 1fb7 2nph 4qlh

(-) Related Entries Specified in the PDB File

4hla WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH DARUNAVIR