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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF77
 
Authors :  C. A. Schiffer, M. N. L. Nalam
Date :  02 Jun 11  (Deposition) - 06 Jun 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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. D. Altman, M. N. L. Nalam, A. Ali, H. Cao, T. M. Rana, C. A. Schiffer, B. Tidor
Protease Inhibitors That Protrude Out From Substrate Envelope Are More Susceptible To Developing Drug Resistance
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPXC35
    Expression System StrainTAP106
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGAG-POL, POL
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    StrainHXB2

 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
177F1Ligand/IonN-[(2S,3R)-4-{(CYCLOHEXYLMETHYL)[(4-METHOXYPHENYL)SULFONYL]AMINO}-3-HYDROXY-1-PHENYLBUTAN-2-YL]-3-HYDROXYBENZAMIDE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , GLY A:16 , GLY A:17 , HOH A:134 , HOH A:154 , GLY B:16 , HOH B:130 , HOH B:131BINDING SITE FOR RESIDUE PO4 A 100
2AC2SOFTWAREGLY A:68 , HIS A:69 , LYS A:70 , HOH A:161 , PRO B:1 , LYS B:55BINDING SITE FOR RESIDUE PO4 A 101
3AC3SOFTWAREASP A:25 , GLY A:27 , ASP A:29 , ASP A:30 , ILE A:47 , GLY A:49 , ILE A:50 , ILE A:84 , HOH A:152 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , VAL B:32 , GLY B:48 , GLY B:49 , ILE B:50 , VAL B:82 , ILE B:84 , HOH B:103BINDING SITE FOR RESIDUE 77F B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SAA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SAA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SAA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SAA)

(-) Exons   (0, 0)

(no "Exon" information available for 3SAA)

(-) 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 O38732_9HIV1 | O38732 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38732_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d3saaa_ A: 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......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3saa A  1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with O38732_9HIV1 | O38732 from UniProtKB/TrEMBL  Length:99

    Alignment length:99
                                    10        20        30        40        50        60        70        80        90         
          O38732_9HIV1    1 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
               SCOP domains d3saab_ 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......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3saa 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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SAA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SAA)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O38732_9HIV1 | O38732)
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
        O38732_9HIV1 | O387322i0a 2i0d 2nxd 2nxl 2nxm 2psu 2psv 2q3k 2q54 2q55 2q5k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3gi4 3gi5 3gi6
UniProtKB/TrEMBL
        O38732_9HIV1 | O387323dck 3dcr 3hzc 3i2l 3ia9 3sa3 3sa4 3sa5 3sa6 3sa7 3sa8 3sa9 3sab 3sac

(-) Related Entries Specified in the PDB File

3sa3 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AG23
3sa4 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF72
3sa5 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF69
3sa6 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF71
3sa7 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF55
3sa8 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH KB83
3sa9 WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF68
3sab WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF78
3sac WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH AF80