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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MULTI-DRUG RESISTANT MUTANT SUBTYPE B 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 :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multi-Drug Resistant Mutant Subtype B Hiv Protease, Tl-3 Inhibitor, 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 - PROTEASE
    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: RESIDUES 1-99
    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  (2, 3)

Asymmetric/Biological Unit (2, 3)
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
2CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:23 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , ARG A:45 , MET 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 , HOH A:233 , LEU B:23 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , ARG B:45 , MET B:46 , ILE B:47 , GLY B:48 , GLY B:49 , ILE B:50 , PHE B:53 , PRO B:81 , ILE B:84BINDING SITE FOR RESIDUE 3TL A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P3A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P3A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P3A)

(-) Exons   (0, 0)

(no "Exon" information available for 2P3A)

(-) 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 Q6BB74_9HIV1 | Q6BB74 from UniProtKB/TrEMBL  Length:317

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q6BB74_9HIV1    1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGKWRPRMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPTPANIIGRNLMTQIGCTLNF 99
               SCOP domains d2p3aa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2p3aA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeee....eeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2p3a A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMALPGKWKPRMIGGIGGFVKVRQYDQIPIEIcGHKVIGTVLVGPTPANIIGRNLMTQIGCTLNF 99
                                    10        20        30        40        50        60      | 70        80        90         
                                                                                             67-CME                            


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q6BB74_9HIV1 | Q6BB74 from UniProtKB/TrEMBL  Length:317

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q6BB74_9HIV1    1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGKWRPRMIGGIGGFVKVRQYDQIPIEICGHKVIGTVLVGPTPANIIGRNLMTQIGCTLNF 99
               SCOP domains d2p3ab_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2p3aB00 B:1-99 Acid Proteases                                                                       CATH domains
           Pfam domains (1) ---RVP-2p3aB01 B:4-98                                                                             - Pfam domains (1)
           Pfam domains (2) ---RVP-2p3aB02 B:4-98                                                                             - Pfam domains (2)
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeee....eeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2p3a B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMALPGKWKPRMIGGIGGFVKVRQYDQIPIEIcGHKVIGTVLVGPTPANIIGRNLMTQIGCTLNF 99
                                    10        20        30        40        50        60      | 70        80        90         
                                                                                             67-CME
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6BB74_9HIV1 | Q6BB74)
molecular function
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    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:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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