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(-) Description

Title :  2.35A RESOLUTION STRUCTURE OF NOROVIRUS 3CL PROTEASE IN COMPLEX AN OXADIAZOLE-BASED, CELL PERMEABLE MACROCYCLIC (21-MER) INHIBITOR
 
Authors :  S. Lovell, K. P. Battaile, N. Mehzabeen, V. C. Damalanka, Y. Kim, K. R. Al P. M. Weerawarna, A. C. G. Kankanamalage, G. H. Lushington, K. -O. Chan W. C. Groutas
Date :  27 Aug 15  (Deposition) - 10 Feb 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protease, Norovirus, Norwalk Virus, Antiviral Inhibitors, Oxadiazole Inhibitor, Cell Permeable, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. C. Damalanka, Y. Kim, K. R. Alliston, P. M. Weerawarna, A. C. Galasiti Kankanamalage, G. H. Lushington, N. Mehzabeen, K. P. Battaile, S. Lovell, K. O. Chang, W. C. Groutas
Oxadiazole-Based Cell Permeable Macrocyclic Transition Stat Inhibitors Of Norovirus 3Cl Protease.
J. Med. Chem. V. 59 1899 2016
PubMed-ID: 26823007  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01464

(-) Compounds

Molecule 1 - 3C-LIKE PROTEASE
    Chains: A, B
    EC Number: 3.4.22.66
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1101-1281
    Gene: ORF1
    Organism Common: HU/NV/NV/1968/US
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 524364
    Strain: GI/HUMAN/UNITED STATES/NORWALK/1968

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2V661Ligand/IonTERT-BUTYL [(4S,7S,10S)-7-(CYCLOHEXYLMETHYL)-10-(HYDROXYMETHYL)-5,8,13-TRIOXO-23-OXA-6,9,14,21,22-PENTAAZABICYCLO[18.2.1]TRICOSA-1(22),20-DIEN-4-YL]CARBAMATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2V661Ligand/IonTERT-BUTYL [(4S,7S,10S)-7-(CYCLOHEXYLMETHYL)-10-(HYDROXYMETHYL)-5,8,13-TRIOXO-23-OXA-6,9,14,21,22-PENTAAZABICYCLO[18.2.1]TRICOSA-1(22),20-DIEN-4-YL]CARBAMATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2V66-1Ligand/IonTERT-BUTYL [(4S,7S,10S)-7-(CYCLOHEXYLMETHYL)-10-(HYDROXYMETHYL)-5,8,13-TRIOXO-23-OXA-6,9,14,21,22-PENTAAZABICYCLO[18.2.1]TRICOSA-1(22),20-DIEN-4-YL]CARBAMATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8binding site for residue CL A 201
2AC2SOFTWARESER A:7 , LYS A:88 , CL B:201 , HOH B:319binding site for residue CL A 202
3AC3SOFTWAREHIS A:30 , GLU A:54 , GLN A:110 , THR A:134 , PRO A:136 , CYS A:139 , HIS A:157 , ALA A:158 , ALA A:159 , ALA A:160 , LYS A:162binding site for residue V66 A 203
4AC4SOFTWARECL A:202 , HOH A:320 , TRP B:6 , SER B:7 , LYS B:88binding site for residue CL B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DG6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DG6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DG6)

(-) Exons   (0, 0)

(no "Exon" information available for 5DG6)

(-) Sequences/Alignments

Asymmetric 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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhheeee..eeeee....eeeee.hhh.....ee..ee.hhheeeee..eeeee............ee........eeeeeee.....eeeeeeeeeeeeeeee..eeeeeeeeee....hhhhh..eeeee....eeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg6 A   0 HAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRIQGRLVHGQSGMLLLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKSGNTVVCAVQA 173
                                     9        19        29        39        49        59        69        79        89        99       109       119  ||   138       148       158       168     
                                                                                                                                                    122|                                         
                                                                                                                                                     132                                         


Chain B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.eeee..eeeee....eeee.hhhh.....ee..ee...eeeee....eeeee...........ee........eeeeeee.....eeeeeeeeeeeee...eeeeeee...hhhhh..eeeeee..eeeeeeeeeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg6 B  -1 HHAPPTLWSRVTKFGSGWGFWVSPTVFITTTHVVPTGVKEFFGEPLSSIAIHQAGEFTQFRFSKKMRPDLTGMVLEEGCPEGTVCSVLIKRDSGELLPLAVRMGAIASMRVHGQSGMLLGTIPGDCGAPYVHKRGNDWVVCGVHAAATKTVVCAVQA 173
                                     8        18        28        38        48        58        68        78        88        98       108|      133       143       153       166       
                                                                                                                                       108|     122|                          162|       
                                                                                                                                        114      133                           166
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DG6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DG6)

(-) Gene Ontology  (22, 22)

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  5dg6
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  POLG_NVN68 | Q83883
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLG_NVN68 | Q83883: 2fyq 2fyr 2lnc 3ur6 3ur9 4imq 4imz 4in1 4in2 4inh 4xbb 4xbc 4xbd 5dgj 5e0g 5e0h 5e0j 5t6d 5t6f 5t6g 5tg1 5tg2

(-) Related Entries Specified in the PDB File

5dgj