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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS PAPAIN-LIKE PROTEASE BOUND TO UBIQUITIN VARIANT ME.4
 
Authors :  B. A. Bailey-Elkin, B. L. Mark
Date :  16 Mar 17  (Deposition) - 10 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plpro, Ubiquitin, Dub, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhang, B. A. Bailey-Elkin, R. C. M. Knaap, B. Khare, T. J. Dalebout, G. G. Johnson, P. B. Van Kasteren, N. J. Mcleish, J. Gu, W. He, M. Kikkert, B. L. Mark, S. S. Sidhu
Potent And Selective Inhibition Of Pathogenic Viruses By Engineered Ubiquitin Variants.
Plos Pathog. V. 13 06372 2017
PubMed-ID: 28542609  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1006372

(-) Compounds

Molecule 1 - MERS-COV PLPRO
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1480-1803
    Gene: ORF1AB
    Organism Scientific: HUMAN BETACORONAVIRUS 2C EMC/2012
    Organism Taxid: 1235996
 
Molecule 2 - ME.4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
3PGO2Ligand/IonS-1,2-PROPANEDIOL
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1672 , CYS A:1675 , CYS A:1707 , CYS A:1709binding site for residue ZN A 1901
2AC2SOFTWAREHOH A:2051 , HOH A:2079binding site for residue NA A 1903
3AC3SOFTWAREALA A:1538 , ASP A:1539 , PRO A:1558binding site for residue PGO A 1904
4AC4SOFTWAREPRO A:1555 , VAL A:1556 , ASP A:1557 , ARG A:1563 , ALA A:1635 , ASN A:1638binding site for residue PGO A 1905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V69)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V69)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V69)

(-) Exons   (0, 0)

(no "Exon" information available for 5V69)

(-) 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:322
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eeeeee...hhhhhh..eee..ee......hhhhh..eeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eeee..eeee.....hhhhhhhhhhhh....eee.hhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhh.eee....eeeeeeee...eeeeeeee.hhh.eee...hhhhhh..eeee.....eeeeeeeeee..eeeeeeeeeeeeee........eeeeee.......eeeeeeee..eeeee....eeee.eeeeeeeeeeee..eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5v69 A 1481 QQLTIEVLVTVDGVNFRTVVLNNKNTYRSQLGCVFFNGADISDTIPDEKQNGHSLYLADNLTADETKALKELYGPVDPTFLHRFYSLKAAVHGWKMVVCDKVRSLKLSDNNCYLNAVIMTLDLLKDIKFVIPALQHAFMKHKGGDSTDFIALIMAYGNCTFGAPDDASRLLHTVLAKAELCCSARMVWREWCNVCGIKDVVLQGLKACCYVGVQTVEDLRARMTYVCQCGGERHRQLVEHTTPWLLLSGTPNEKLVTTSTAPDFVAFNVFQGIETAVGHYVHARLKGGLILKFDSGTVSKTSDWKCKVTDVLFPGQKYSSDC 1802
                                  1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710      1720      1730      1740      1750      1760      1770      1780      1790      1800  


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                         
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...eeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                5v69 B    1 MRIFVETLTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFFGQQLEDGRTLSDYNIVKYSTLHLILRLNS   75
                                  ||13        23        33        43        53        63        73  
                                  7|                                                                
                                  11
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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  (0, 0)

(no "SCOP Domain" information available for 5V69)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V69)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V69)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  5v69
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 Related Entries

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

UniProtKB/Swiss-Prot
        K0BWD0_9BETC | K0BWD0: 5v6a 5wwp
UniProtKB/TrEMBL
        K0BWD0_9BETC | K0BWD0: 4p16

(-) Related Entries Specified in the PDB File

5v6a