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(-) Description

Title :  CRYSTAL STRUCTURES OF A MULTIDRUG-RESISTANT HIV-1 PROTEASE REVEAL AN EXPANDED ACTIVE SITE CAVITY
 
Authors :  B. C. Logsdon, J. F. Vickrey, P. Martin, G. Proteasa, J. I. Koepke, S. R. Terlecky, Z. Wawrzak, M. A. Winters, T. C. Merigan, L. C. Kovari
Date :  12 Dec 03  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv Protease, Aids, Polyprotein, Hydrolase, Aspartyl Protease, Multi-Drug Resistance, Lopinavir (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. C. Logsdon, J. F. Vickrey, P. Martin, G. Proteasa, J. I. Koepke, S. R. Terlecky, Z. Wawrzak, M. A. Winters, T. C. Merigan, L. C. Kovari
Crystal Structures Of A Multidrug-Resistant Human Immunodeficiency Virus Type 1 Protease Reveal An Expanded Active-Site Cavity.
J. Virol. V. 78 3123 2004
PubMed-ID: 14990731  |  Reference-DOI: 10.1128/JVI.78.6.3123-3132.2004
(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: PJFV769NOHIS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HIV-1
    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
1AB11Ligand/IonN-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:25 , GLY A:27 , GLN A:61 , THR A:80 , PRO A:81 , ALA A:82 , VAL A:84 , LEU B:23 , THR B:80 , PRO B:81 , ALA B:82 , VAL B:84BINDING SITE FOR RESIDUE AB1 B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RV7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RV7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RV7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RV7)

(-) Exons   (0, 0)

(no "Exon" information available for 1RV7)

(-) 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 Q9QM22_9HIV1 | Q9QM22 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q9QM22_9HIV1    1 PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPANIIGRNLMTQIGCTLNF 99
               SCOP domains d1rv7a_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 1rv7A00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeee..eeeeeeee......ee.........eeeeee....eeeeeeeeeeeeee..eeeeeeeee......eeehhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  1rv7 A  1 PQITLWQRPIVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPANVIGRNLMTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q9QM22_9HIV1 | Q9QM22 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q9QM22_9HIV1    1 PQITLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPANIIGRNLMTQIGCTLNF 99
               SCOP domains d1rv7b_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 1rv7B00 B:1-99 Acid Proteases                                                                       CATH domains
           Pfam domains (1) ---RVP-1rv7B01 B:4-98                                                                             - Pfam domains (1)
           Pfam domains (2) ---RVP-1rv7B02 B:4-98                                                                             - Pfam domains (2)
         Sec.struct. author .ee......eeeehhhhh.eeeee.......ee.........eeeee......eeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  1rv7 B  1 PQITLWQRPIVTIKIGGQLKEALLNTGADDTVLEEVNLPGRWKPKLIGGIGGFVKVRQYDQVPIEICGHKVIGTVLVGPTPANVIGRNLMTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
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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   (Q9QM22_9HIV1 | Q9QM22)
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

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

UniProtKB/Swiss-Prot
        Q9QM22_9HIV1 | Q9QM22: 3ots
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        Q9QM22_9HIV1 | Q9QM22: 1rpi 4gye 4gzf

(-) Related Entries Specified in the PDB File

1rpi 1rq9