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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH MKP97
 
Authors :  C. A. Schiffer, M. N. L. Nalam
Date :  02 Feb 12  (Deposition) - 01 Aug 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1 Protease, Drug Resistance, Drug Design, Protease Inhibitors, Aids, Aspartyl Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Parai, D. J. Huggins, H. Cao, M. N. Nalam, A. Ali, C. A. Schiffer, B. Tidor, T. M. Rana
Design, Synthesis, And Biological And Structural Evaluation Of Novel Hiv-1 Protease Inhibitors To Combat Drug Resistance.
J. Med. Chem. V. 55 6328 2012
PubMed-ID: 22708897  |  Reference-DOI: 10.1021/JM300238H

(-) Compounds

Molecule 1 - POL POLYPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC35
    Expression System Strain: TAP56
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-99
    Gene: GAG-POL, POL
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: SF2
    Synonym: HIV-1 PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
10KJ1Ligand/Ion[(2S)-5-OXOPYRROLIDIN-2-YL]METHYL [(2S,3R)-4-{(1,3-BENZOTHIAZOL-6-YLSULFONYL)[(2S)-2-METHYLBUTYL]AMINO}-3-HYDROXY-1-PHENYLBUTAN-2-YL]CARBAMATE
2PO43Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , GLY A:48 , ILE A:50 , HOH A:201 , HOH A:222 , HOH A:268 , 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 0KJ A 101
2AC2SOFTWAREMET A:36 , ASN A:37 , HOH A:257 , PRO B:39 , GLY B:40BINDING SITE FOR RESIDUE PO4 A 102
3AC3SOFTWAREGLY A:68 , HIS A:69 , LYS A:70 , HOH A:243 , PRO B:1 , LYS B:55BINDING SITE FOR RESIDUE PO4 B 101
4AC4SOFTWAREARG A:14 , GLY A:16 , GLY A:17 , HOH A:253 , GLY B:16 , GLY B:17 , HOH B:219 , HOH B:228BINDING SITE FOR RESIDUE PO4 B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DJR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DJR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DJR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DJR)

(-) Exons   (0, 0)

(no "Exon" information available for 4DJR)

(-) 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 Q90K99_9HIV1 | Q90K99 from UniProtKB/TrEMBL  Length:400

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q90K99_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d4djra_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4djr A  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q90K99_9HIV1 | Q90K99 from UniProtKB/TrEMBL  Length:400

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          Q90K99_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d4djrb_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4djr B  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 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  (0, 0)

(no "CATH Domain" information available for 4DJR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DJR)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q90K99_9HIV1 | Q90K99)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        Q90K99_9HIV1 | Q90K99: 3o9f 3o9g 3o9h 3o9i 3r4b
UniProtKB/TrEMBL
        Q90K99_9HIV1 | Q90K99: 3o99 3o9a 3o9b 3o9c 3o9d 3o9e 4djo 4djp 4djq

(-) Related Entries Specified in the PDB File

4djo 4djp 4djq