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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DESMOCOLLIN-2 ECTODOMAIN FRAGMENT EC2-5
 
Authors :  O. J. Harrison, J. Brasch, L. Shapiro
Date :  14 Nov 15  (Deposition) - 15 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
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 - DESMOCOLLIN-2
    ChainsA, B
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System Taxid9606
    FragmentUNP RESIDUES 236-680
    GeneDSC2, CDHF2, DSC3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCADHERIN FAMILY MEMBER 2,DESMOCOLLIN-3,DESMOSOMAL GLYCOPROTEIN II,DESMOSOMAL GLYCOPROTEIN III

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 51)

Asymmetric/Biological Unit (6, 51)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CA21Ligand/IonCALCIUM ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4MAN11Ligand/IonALPHA-D-MANNOSE
5NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (42, 42)

Asymmetric Unit (42, 42)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , HIS A:142 , ASP A:192binding site for residue CA A 811
02AC2SOFTWAREGLU A:119 , ASP A:177 , GLU A:179 , ASP A:215 , HOH A:901 , HOH A:935binding site for residue CA A 812
03AC3SOFTWAREGLU A:119 , GLU A:179 , ASP A:212 , VAL A:213 , ASP A:215 , ASP A:247binding site for residue CA A 813
04AC4SOFTWAREGLU A:231 , ASN A:232 , ASN A:289 , GLU A:291 , GLU A:332 , HOH A:938binding site for residue CA A 814
05AC5SOFTWAREGLU A:231 , GLU A:291 , ASP A:329 , GLN A:330 , GLU A:332 , GLU A:364binding site for residue CA A 815
06AC6SOFTWAREASN A:214 , HIS A:216 , ASP A:245 , ASP A:247 , ASN A:253 , ASN A:304binding site for residue CA A 816
07AC7SOFTWAREGLU A:347 , GLU A:401 , ASP A:434 , VAL A:435 , ASP A:437 , ASP A:465binding site for residue CA A 817
08AC8SOFTWAREGLU A:347 , ASP A:399 , GLU A:401 , ASP A:437 , HOH A:923binding site for residue CA A 818
09AC9SOFTWAREASP A:331 , GLU A:332 , ASP A:362 , GLU A:364 , HOH A:912binding site for residue CA A 819
10AD1SOFTWAREASN A:436 , ASN A:438 , ASP A:463 , ASP A:465 , HIS A:469 , ASP A:519binding site for residue CA A 820
11AD2SOFTWARECYS A:131binding site for residue SO4 A 821
12AD3SOFTWAREVAL A:153 , LYS A:183 , GLN A:185binding site for residue EDO A 822
13AD4SOFTWAREASP A:103 , GLN A:485binding site for residue EDO A 823
14AD5SOFTWAREASN A:268 , GLU A:292 , LYS A:293binding site for residue EDO A 824
15AD6SOFTWAREASN B:102 , ASN B:104 , ASP B:134 , ASP B:136 , HIS B:142 , ASP B:192binding site for residue CA B 614
16AD7SOFTWAREGLU B:119 , GLU B:179 , ASP B:212 , VAL B:213 , ASP B:215 , ASP B:247binding site for residue CA B 615
17AD8SOFTWAREGLU B:119 , ASP B:177 , GLU B:179 , ASP B:215 , HOH B:706 , HOH B:732binding site for residue CA B 616
18AD9SOFTWAREASN B:214 , HIS B:216 , ASP B:245 , ASP B:247 , ASN B:253 , ASN B:304binding site for residue CA B 617
19AE1SOFTWAREGLU B:231 , ASN B:289 , GLU B:291 , GLU B:332 , HOH B:702binding site for residue CA B 618
20AE2SOFTWAREGLU B:231 , GLU B:291 , ASP B:329 , GLN B:330 , GLU B:332 , GLU B:364binding site for residue CA B 619
21AE3SOFTWAREASP B:331 , GLU B:332 , ASP B:362 , GLU B:364 , HOH B:721binding site for residue CA B 620
22AE4SOFTWAREGLU B:347 , ASP B:399 , GLU B:401 , ASP B:437 , HOH B:714 , HOH B:731binding site for residue CA B 621
23AE5SOFTWAREGLU B:347 , GLU B:401 , ASP B:434 , VAL B:435 , ASP B:437 , ASP B:465binding site for residue CA B 622
24AE6SOFTWAREASN B:436 , ASN B:438 , ASP B:463 , ASP B:465 , HIS B:469 , ASP B:519binding site for residue CA B 623
25AE7SOFTWAREGLU A:279 , ASP B:329binding site for residue CA B 624
26AE8SOFTWAREVAL B:272 , CYS B:283binding site for residue SO4 B 625
27AE9SOFTWAREILE B:260 , LEU B:261 , ASN B:264binding site for residue EDO B 626
28AF1SOFTWAREILE B:340 , ASN B:411 , GLY B:429 , NAG B:602binding site for residue EDO B 627
29AF2SOFTWAREILE A:150 , GLY A:151 , LEU A:186 , ILE A:188 , THR A:203 , SER A:204 , MAN A:802binding site for Poly-Saccharide residues LYS A 187 through MAN A 801 bound to THR A 203
30AF3SOFTWARETHR A:205 , MAN A:801binding site for Mono-Saccharide MAN A 802 bound to THR A 205
31AF4SOFTWAREASN A:257binding site for Mono-Saccharide NAG A 805 bound to ASN A 257
32AF5SOFTWARELYS A:406 , ASN A:407 , ILE A:409 , ASN A:411binding site for Poly-Saccharide residues NAG A 806 through MAN A 809 bound to ASN A 411
33AF6SOFTWARETHR A:423 , PHE B:395binding site for Mono-Saccharide MAN A 803 bound to THR A 423
34AF7SOFTWARETHR A:425binding site for Mono-Saccharide MAN A 804 bound to THR A 425
35AF8SOFTWAREGLU A:458 , ILE A:493 , ASN A:494 , THR A:496 , ALA A:498binding site for Poly-Saccharide residues ALA A 497 through NAG A 810 bound to ASN A 494
36AF9SOFTWARELYS B:187 , THR B:203 , MAN B:610binding site for Mono-Saccharide MAN B 611 bound to THR B 203
37AG1SOFTWARETHR B:112 , THR B:205 , MAN B:611binding site for Mono-Saccharide MAN B 610 bound to THR B 205
38AG2SOFTWAREASN B:257binding site for Mono-Saccharide NAG B 601 bound to ASN B 257
39AG3SOFTWARELYS B:406 , ASN B:407 , ILE B:409 , ASN B:411 , EDO B:627binding site for Poly-Saccharide residues NAG B 602 through MAN B 605 bound to ASN B 411
40AG4SOFTWAREPHE A:395 , THR B:423 , MAN B:613binding site for Mono-Saccharide MAN B 612 bound to THR B 423
41AG5SOFTWARETHR B:425 , MAN B:612 , HOH B:704binding site for Mono-Saccharide MAN B 613 bound to THR B 425
42AG6SOFTWAREGLU B:458 , VAL B:460 , ASN B:494 , ALA B:497binding site for Poly-Saccharide residues NAG B 606 through MAN B 609 bound to ASN B 494

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:336 -A:424
2A:450 -A:536
3A:534 -A:542
4B:336 -B:424
5B:450 -B:536
6B:534 -B:542

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val A:153 -Pro A:154
2Ser A:156 -Pro A:157
3Asn A:337 -Pro A:338
4Pro A:471 -Pro A:472
5Val B:153 -Pro B:154
6Ser B:156 -Pro B:157
7Asn B:337 -Pro B:338
8Pro B:471 -Pro B:472

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERP)

(-) 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:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...eeeeeee.......eeee..eee.....hhhhh.eeeeeeee......eee.....eeee...........eeeeeeeee.hhhh....eeeeeeeeeee.......ee...eeeeeee.....eeeeee.ee...........eeeeeee......eeeee......eeeee..........eeeeeeeeee..............eeeeeeeeee...........eeeeeee.......ee...........................eee......eee..............eeeeeeeee.....eeeeeeeeeee......................eeeee.....hhhhh...eee............eeee....eeeee...........eeeeee.....eeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erp A 101 ENDNYPIFTEETYTFTIFENCRVGTTVGQVCATDKDEPDTMHTRLKYSIIGQVPPSPTLFSMHPTTGVITTTSSQLDRELIDKYQLKIKVQDMDGQYFGLQTTSTCIINIDDVNDHLPTFTRTSYVTSVEENTVDVEILRVTVEDKDLVNTANWRANYTILKGNENGNFKIVTDAKTNEGVLCVVKPLNYEEKQQMILQIGVVNEAPFSREASPRSAMSTATVTVNVEDQDEGPECNPPIQTVRMKENAEVGTTSNGYKAYDPETRSSSGIRYKKLTDPTGWVTIDENTGSIKVFRSLDREAETIKNGIYNITVLASDQGGRTCTGTLGIILQDVNDNSPFIPKKTVIICKPTMSSAEIVAVDPDEPIHGPPFDFSLESSTSEVQRMWRLKAINDTAARLSYQNDPPFGSYVVPITVRDRLGMSSVTSLDVTLCDCITENDCT 543
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540   

Chain B from PDB  Type:PROTEIN  Length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...eeeeeee.......eeee..eee.....hhhhh.eeeeeeee......eee.....eeee...........eeeeeeeee.hhhh....eeeeeeeeeee.......ee...eeeeeee.....eeeeee.ee...........eeeeeee......eeeee......eeeee..........eeeeeeeeee........eeeeeeeeee...........eeeeeee.......ee...........................eee......eee..............eeeeeeeee.....eeeeeeeeeee............eee.......eeeee.....hhhhh...eee...........eeeee....eeeeee..........eeeeee.....eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5erp B 101 ENDNYPIFTEETYTFTIFENCRVGTTVGQVCATDKDEPDTMHTRLKYSIIGQVPPSPTLFSMHPTTGVITTTSSQLDRELIDKYQLKIKVQDMDGQYFGLQTTSTCIINIDDVNDHLPTFTRTSYVTSVEENTVDVEILRVTVEDKDLVNTANWRANYTILKGNENGNFKIVTDAKTNEGVLCVVKPLNYEEKQQMILQIGVVNEAPFSRAMSTATVTVNVEDQDEGPECNPPIQTVRMKENAEVGTTSNGYKAYDPETRSSSGIRYKKLTDPTGWVTIDENTGSIKVFRSLDREAETIKNGIYNITVLASDQGGRTCTGTLGIILQDVNDNSPFIPKKTVIICKPTMSSAEIVAVDPDEPIHGPPFDFSLESSTSEVQRMWRLKAINDTAARLSYQNDPPFGSYVVPITVRDRLGMSSVTSLDVTLCDCITENDCTH 544
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310|      326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536        
                                                                                                                                                                                                                                           310|                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                            317                                                                                                                                                                                                                                   

   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 5ERP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DSC2_HUMAN | Q024875j5j

(-) Related Entries Specified in the PDB File

5eqx 5EQX CONTAINS A RELATED DESMOSOMAL CADHERIN
5erd 5ERD CONTAINS A RELATED DESMOSOMAL CADHERIN