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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MULTI-DRUG RESISTANT MUTANT SUBTYPE F HIV PROTEASE COMPLEXED WITH TL-3 INHIBITOR
 
Authors :  M. Sanches, S. Krauchenco, N. H. Martins, A. Gustchina, A. Wlodawer, I. Polikarpov
Date :  08 Mar 07  (Deposition) - 24 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multi-Drug Resistant Mutant Subtype F Hiv Protease, Tl-3 Inhibitor, Non-B Hiv Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sanches, S. Krauchenco, N. H. Martins, A. Gustchina, A. Wlodawer, I. Polikarpov
Structural Characterization Of B And Non-B Subtypes Of Hiv-Protease: Insights Into The Natural Susceptibility To Drug Resistance Development.
J. Mol. Biol. V. 369 1029 2007
PubMed-ID: 17467738  |  Reference-DOI: 10.1016/J.JMB.2007.03.049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POL PROTEIN
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HIV-1 PROTEASE
    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
13TL1Ligand/IonBENZYL [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-DIBENZYL-8,9-DIHYDROXY-1,16-DIMETHYL-4,13-BIS(1-METHYLETHYL)-2,5,12,15,18-PENTAOXO-20-PHENYL-19-OXA-3,6,11,14,17-PENTAAZAICOS-1-YL]CARBAMATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , VAL A:32 , ILE A:46 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , PHE A:53 , PRO A:81 , ILE A:84 , HOH A:202 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , VAL B:32 , ILE B:46 , ILE B:47 , GLY B:48 , GLY B:49 , ILE B:50 , PHE B:53 , PRO B:81 , ALA B:82 , ILE B:84 , HOH B:113BINDING SITE FOR RESIDUE 3TL A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P3D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P3D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P3D)

(-) Exons   (0, 0)

(no "Exon" information available for 2P3D)

(-) 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 Q7SRY5_9HIV1 | Q7SRY5 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q7SRY5_9HIV1    1 PQNTLWQRPIVTIKVEGQLREALLDTGADDTVLEDINLSGKWKPKIIGGIRGFVKVKQYEDILIEICGHRAVGAVLVGPTPANIIGRNMLTQIGCTLNF 99
               SCOP domains d2p3da_ A: automated matches                                                                        SCOP domains
               CATH domains 2p3dA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeee....eeeeee.......ee.........eeeeee....eeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2p3d A  1 PQITLWKRPIVTIKVEGQLREALLDTGADDTVLEDINLSGKWKPKIIGGIRGFVKVKQYEDILIEICGHRAVGAVLVGPTPANIIGRNMLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q7SRY5_9HIV1 | Q7SRY5 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q7SRY5_9HIV1    1 PQNTLWQRPIVTIKVEGQLREALLDTGADDTVLEDINLSGKWKPKIIGGIRGFVKVKQYEDILIEICGHRAVGAVLVGPTPANIIGRNMLTQIGCTLNF 99
               SCOP domains d2p3db_ B: automated matches                                                                        SCOP domains
               CATH domains 2p3dB00 B:1-99 Acid Proteases                                                                       CATH domains
           Pfam domains (1) ---RVP-2p3dB01 B:4-98                                                                             - Pfam domains (1)
           Pfam domains (2) ---RVP-2p3dB02 B:4-98                                                                             - Pfam domains (2)
         Sec.struct. author .ee......eeeeee..eeeeeee.......eee........eeeeee....eeeeeeeeeeeeee..eeeeeeeeee....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2p3d B  1 PQITLWKRPIVTIKVEGQLREALLDTGADDTVLEDINLSGKWKPKIIGGIRGFVKVKQYEDILIEICGHRAVGAVLVGPTPANIIGRNMLTQIGCTLNF 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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_AA (368)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7SRY5_9HIV1 | Q7SRY5)
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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 Related Entries

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(-) Related Entries Specified in the PDB File

2p3a CRYSTAL STRUCTURE OF THE MULTI-DRUG RESISTANT MUTANT SUBTYPE B HIV PROTEASE COMPLEXED WITH TL-3 INHIBITOR
2p3b CRYSTAL STRUCTURE OF THE SUBTYPE B WILD TYPE HIV PROTEASE COMPLEXED WITH TL-3 INHIBITOR
2p3c CRYSTAL STRUCTURE OF THE SUBTYPE F WILD TYPE HIV PROTEASE COMPLEXED WITH TL-3 INHIBITOR