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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF HIV-1 PROTEASE IRM MUTANT COMPLEXED WITH ATAZANAVIR (BMS-232632)
 
Authors :  H. E. Klei, S. Sheriff
Date :  04 Feb 06  (Deposition) - 20 Feb 07  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Immunodeficiency Virus (Hiv), Hiv-1 Protease, Reyataz, Atazanavir, Bms-232632, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. E. Klei, K. Kish, P. F. Lin, Q. Guo, J. Friborg, R. E. Rose, Y. Zhang, V. Goldfarb, D. R. Langley, M. Wittekind, S. Sheriff
X-Ray Crystal Structures Of Human Immunodeficiency Virus Type 1 Protease Mutants Complexed With Atazanavir.
J. Virol. V. 81 9525 2007
PubMed-ID: 17537865  |  Reference-DOI: 10.1128/JVI.02503-05
(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: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HIV-1 PROTEASE
    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  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2DR71Ligand/Ion(3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5,6,10,13-PENTAAZATETRADECANEDIOICACID DIMETHYL ESTER
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:1 , LYS A:55 , HOH A:150 , HOH A:168 , HOH A:169 , HOH A:171 , LYS B:70 , PHE B:99BINDING SITE FOR RESIDUE SO4 A 100
2AC2SOFTWAREHOH A:114BINDING SITE FOR RESIDUE ACT A 101
3AC3SOFTWAREARG A:8 , ILE A:10 , LEU A:23 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , GLY A:48 , GLY A:49 , ILE A:50 , PHE A:82 , VAL A:84 , HOH A:104 , HOH A:157 , ARG B:8 , ASP B:25 , GLY B:27 , ASP B:29 , GLY B:48 , GLY B:49 , HOH B:100BINDING SITE FOR RESIDUE DR7 A 102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FXD)

(-) 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 Q90HG9_9HIV1 | Q90HG9 from UniProtKB/TrEMBL  Length:371

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q90HG9_9HIV1    1 PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKIIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNVIGRNLMTQIGCTLNF 99
               SCOP domains d2fxda_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2fxdA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......eee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2fxd A  1 PQITLWKRPIVTVKIGGQLKEALLDTGADDTVIEEMNLPGKWKPKIIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPFNVIGRNLMTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q90HG9_9HIV1 | Q90HG9 from UniProtKB/TrEMBL  Length:371

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q90HG9_9HIV1    1 PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKIIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNVIGRNLMTQIGCTLNF 99
               SCOP domains d2fxdb_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 2fxdB00 B:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  2fxd B  1 PQITLWKRPIVTVKIGGQLKEALLDTGADDTVIEEMNLPGKWKPKIIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPFNVIGRNLMTQIGATLNF 99
                                    10        20        30        40        50        60        70        80        90
   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  (0, 0)

(no "Pfam Domain" information available for 2FXD)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q90HG9_9HIV1 | Q90HG9)
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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2fxe X-RAY CRYSTAL STRUCTURE OF A CLEAVAGE-RESISTANT MUTANT (CRM) OF HIV-1 PROTEASE WITH ATAZANAVIR (BMS-232632)