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(-) Description

Title :  HIV PROTEASE COMPLEXED WITH COMPOUND 10B
 
Authors :  H. P. Su
Date :  22 Mar 10  (Deposition) - 30 Jun 10  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv, Protease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Jones, M. K. Holloway, H. P. Su, S. S. Carroll, C. Burlein, S. Touch D. J. Distefano, R. I. Sanchez, T. M. Williams, J. P. Vacca, C. A. Coburn
Epsilon Substituted Lysinol Derivatives As Hiv-1 Protease Inhibitors.
Bioorg. Med. Chem. Lett. V. 20 4065 2010
PubMed-ID: 20547452  |  Reference-DOI: 10.1016/J.BMCL.2010.05.082

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 7-105
    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, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
15952Ligand/IonN-[(1S,5S)-5-{[(4-AMINOPHENYL)SULFONYL](3-METHYLBUTYL)AMINO}-1-METHYL-6-OXOHEXYL]-NALPHA-(METHOXYCARBONYL)-BETA-PHENYL-L-PHENYLALANINAMIDE
2CL3Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , VAL A:82 , ILE A:84 , ARG B:8 , LEU B:23 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , GLY B:48 , GLY B:49 , ILE B:50 , PRO B:81 , ILE B:84BINDING SITE FOR RESIDUE 595 A 100
2AC2SOFTWARETHR A:74 , ASN A:88 , ARG B:41BINDING SITE FOR RESIDUE CL A 101
3AC3SOFTWAREARG A:8 , ASP A:25 , GLY A:27 , ALA A:28 , ASP A:30 , GLY A:48 , GLY A:49 , ILE A:50 , VAL A:82 , ILE A:84 , LEU B:23 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , ASP B:30 , GLY B:48 , GLY B:49 , ILE B:50 , PRO B:81 , VAL B:82 , ILE B:84 , HOH B:141 , HOH B:154 , HOH B:164BINDING SITE FOR RESIDUE 595 B 100
4AC4SOFTWARETRP B:6BINDING SITE FOR RESIDUE CL B 101
5AC5SOFTWARETHR B:74 , ASN B:88 , HOH B:136BINDING SITE FOR RESIDUE CL B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M9F)

(-) Exons   (0, 0)

(no "Exon" information available for 3M9F)

(-) 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 Q9WFL7_9HIV1 | Q9WFL7 from UniProtKB/TrEMBL  Length:347

    Alignment length:99
                                    16        26        36        46        56        66        76        86        96         
         Q9WFL7_9HIV1     7 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 105
               SCOP domains d3m9fa_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3m9f A   1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
 aligned with Q9WFL7_9HIV1 | Q9WFL7 from UniProtKB/TrEMBL  Length:347

    Alignment length:99
                                    16        26        36        46        56        66        76        86        96         
         Q9WFL7_9HIV1     7 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 105
               SCOP domains d3m9fb_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---RVP-3m9fB01 B:4-98                                                                             - Pfam domains (1)
           Pfam domains (2) ---RVP-3m9fB02 B:4-98                                                                             - Pfam domains (2)
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3m9f B   1 PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  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 3M9F)

(-) 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   (Q9WFL7_9HIV1 | Q9WFL7)
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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  3m9f
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9WFL7_9HIV1 | Q9WFL7: 5hvp
UniProtKB/TrEMBL
        Q9WFL7_9HIV1 | Q9WFL7: 2qmp 4ll3

(-) Related Entries Specified in the PDB File

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