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(-) Description

Title :  TL-3 INHIBITED TRP6ALA HIV PROTEASE WITH 1-BROMO-2-NAPTHOIC ACID BOUND IN EXOSITE
 
Authors :  T. Tiefenbrunn, C. D. Stout
Date :  12 Apr 13  (Deposition) - 18 Sep 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fragment Binding, Exosite, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tiefenbrunn, S. Forli, M. Happer, A. Gonzalez, Y. Tsai, M. Soltis, J. H. Elder, A. J. Olson, C. D. Stout
Crystallographic Fragment-Based Drug Discovery: Use Of A Brominated Fragment Library Targeting Hiv Protease.
Chem. Biol. Drug Des. V. 83 141 2014
PubMed-ID: 23998903  |  Reference-DOI: 10.1111/CBDD.12227

(-) Compounds

Molecule 1 - GAG-POL POLYPROTEIN
    Chains: A, B
    EC Number: 3.4.23.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Strain: ROSETTA2(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11683

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
127B2Ligand/Ion1-BROMONAPHTHALENE-2-CARBOXYLIC ACID
23TL1Ligand/IonBENZYL [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-DIBENZYL-8,9-DIHYDROXY-1,16-DIMETHYL-4,13-BIS(1-METHYLETHYL)-2,5,12,15,18-PENTAOXO-20-PHENYL-19-OXA-3,6,11,14,17-PENTAAZAICOS-1-YL]CARBAMATE
3BR1Ligand/IonBROMIDE ION
4DMS1Ligand/IonDIMETHYL SULFOXIDE
5NO35Ligand/IonNITRATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:12 , GLU A:65 , ILE A:66 , CYS A:67 , GLY A:68BINDING SITE FOR RESIDUE DMS A 101
02AC2SOFTWARELYS A:14 , PHE A:53 , LEU A:63 , LYS A:70 , HOH A:219BINDING SITE FOR RESIDUE 27B A 102
03AC3SOFTWAREGLU A:35 , TRP A:42 , LYS A:55 , VAL A:56 , ARG A:57 , VAL A:77 , GLY A:78 , PRO A:79BINDING SITE FOR RESIDUE NO3 A 103
04AC4SOFTWAREPRO A:39 , ARG A:41 , PHE A:53 , ILE A:62 , LEU A:63 , HOH A:212 , HOH A:233BINDING SITE FOR RESIDUE NO3 A 104
05AC5SOFTWAREPRO A:39 , GLY A:40 , ARG A:41 , PHE A:53 , ILE A:54 , LYS A:55BINDING SITE FOR RESIDUE NO3 A 105
06AC6SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , MET A:46 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , PRO A:81 , VAL A:82 , HOH A:217 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , GLY B:48 , GLY B:49 , ILE B:50 , PHE B:53 , PRO B:81 , 27B B:102BINDING SITE FOR RESIDUE 3TL A 106
07AC7SOFTWARETHR B:12 , LYS B:14 , GLU B:65 , CYS B:67 , GLY B:68BINDING SITE FOR RESIDUE NO3 B 101
08AC8SOFTWAREGLY A:48 , 3TL A:106 , ARG B:8 , LYS B:14 , PRO B:81 , HOH B:201BINDING SITE FOR RESIDUE 27B B 102
09AC9SOFTWARELYS B:20 , GLU B:21 , ASN B:83BINDING SITE FOR RESIDUE NO3 B 103
10BC1SOFTWAREPRO B:44BINDING SITE FOR RESIDUE BR B 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K4R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K4R)

(-) Exons   (0, 0)

(no "Exon" information available for 4K4R)

(-) 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
                                                                                                                                  
               SCOP domains d4k4ra_ 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......eehhhhhhhh..eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4k4r A  1 PQITLAKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d4k4rb_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee......eeee........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeeee.....eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4k4r B  1 PQITLAKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 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  (0, 0)

(no "CATH Domain" information available for 4K4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K4R)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  4k4r
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  POL_HV1Z2 | P12499
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  3.4.23.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1Z2 | P12499: 1e28 1hxw 1p7q 1pro 1q94 1vij 1vik 2wkz 2wl0 2xye 2xyf 3kf0 3kfn 3kfp 3kfr 3kfs 3w39 4dqb 4dqc 4dqe 4dqf 4dqg 4dqh 4e43 4ej8 4ejd 4ejk 4ejl 4k4p 4k4q

(-) Related Entries Specified in the PDB File

4k4p 4k4q