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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DESMOGLEIN-3 ECTODOMAIN
 
Authors :  O. J. Harrison, J. Brasch, L. Shapiro
Date :  13 Nov 15  (Deposition) - 15 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Extracellular Cadherin Domain, Cell Adhesion, Cell Surface, Desmosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. J. Harrison, J. Brasch, G. Lasso, P. S. Katsamba, G. Ahlsen, B. Honig L. Shapiro
Structural Basis Of Adhesive Binding By Desmocollins And Desmogleins.
Proc. Natl. Acad. Sci. Usa V. 113 7160 2016
PubMed-ID: 27298358  |  Reference-DOI: 10.1073/PNAS.1606272113

(-) Compounds

Molecule 1 - DESMOGLEIN-3
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Gene: DSG3, CDHF6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 130 KDA PEMPHIGUS VULGARIS ANTIGEN,PVA,CADHERIN FAMILY MEMBER 6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:11 , GLU A:69 , ASP A:100 , ILE A:101 , ASP A:103 , ASP A:136binding site for residue CA A 604
02AC2SOFTWAREASN A:212 , ASN A:214 , ASP A:243 , ASP A:245 , ASN A:251 , ASN A:302binding site for residue CA A 605
03AC3SOFTWAREGLU A:11 , ASP A:67 , GLU A:69 , ASP A:103 , ASN A:104 , HOH A:746binding site for residue CA A 606
04AC4SOFTWAREASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:142 , ASP A:192binding site for residue CA A 607
05AC5SOFTWAREGLU A:119 , ASP A:177 , GLU A:179 , ASP A:213binding site for residue CA A 608
06AC6SOFTWAREGLU A:119 , GLU A:179 , ASP A:210 , VAL A:211 , ASP A:213 , ASP A:245binding site for residue CA A 609
07AC7SOFTWAREGLU A:229 , GLU A:289 , ASN A:327 , VAL A:328 , GLU A:330 , ASP A:366binding site for residue CA A 610
08AC8SOFTWAREGLU A:229 , ASP A:287 , GLU A:289 , GLU A:330binding site for residue CA A 611
09AC9SOFTWAREASN A:19 , ASN A:61binding site for Poly-Saccharide residues NAG A 601 through NAG A 602 bound to ASN A 61
10AD1SOFTWAREASN A:131binding site for Mono-Saccharide NAG A 603 bound to ASN A 131
11AD2SOFTWAREGLY A:425 , THR A:427 , MAN A:612binding site for Mono-Saccharide MAN A 614 bound to THR A 427
12AD3SOFTWAREGLU A:416 , THR A:427 , THR A:429 , MAN A:613 , MAN A:614binding site for Mono-Saccharide MAN A 612 bound to THR A 429
13AD4SOFTWAREALA A:337 , GLU A:416 , THR A:429 , THR A:431 , MAN A:612binding site for Mono-Saccharide MAN A 613 bound to THR A 431

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:19 -Pro A:20
2Pro A:46 -Pro A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EQX)

(-) 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:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....ee...........ee.ee.hhh....eeeee...........eee.....eeee..........eeeeeeeee..........eeeeeeee.......ee...eeeeee........eeee..ee...............eeee.......eee.....eeee...........eeeeeeeee.hhhh..eeeeeeeeee........ee....eeeeee....eeeeeee.ee...........eeeeeee......eeeee......eeeee..........eeeeeeeeee.......hhhhh....eeeeeeee.....ee....eeeee...............ee...ee.........eeeeee.hhhh.eee.....eeee..............eeeeeeeeee......eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5eqx A   1 EWVKFAKPCREGEDNSKRNPIAKITSDYQATQKITYRISGVGIDQPPFGIFVVDKNTGDINITAIVDREETPSFLITCRALNAQGLDVEKPLILTVKILDINDNPPVFSQQIFMGEIEENSASNSLVMILNATDADEPNHLNSKIAFKIVSQEPAGTPMFLLSRNTGEVRTLTNSLDREQASSYRLVVSGADKDGEGLSTQCECNIKVKDVNDNFPMFRDSQYSARIEENILSSELLRFQVTDLDEEYTDNWLAVYFFTSGNEGNWFEIQTDPRTNEGILKVVKALDYEQLQSVKLSIAVKNKAEFHQSVISRYRVQSTPVTIQVINVREGIAFRPASKTFTVQKGISSKKLVDYILGTYQAIDEDTNKAASNVKYVMGRNDGGYLMIDSKTAEIKFVKNMNRDSTFIVNKTITAEVLAIDEYTGKTSTGTVYVRVPDF 439
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   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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5erd 5erp