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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DESMOGLEIN-2 ECTODOMAIN
 
Authors :  J. Brasch, O. J. Harrison, L. Shapiro
Date :  13 Nov 15  (Deposition) - 22 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Extracellular Cadherin Domain, Cell Adhesion, Desmosome, Cell Surface (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-2
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Gene: DSG2, CDHF5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CADHERIN FAMILY MEMBER 5,HDGC

 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
1BMA4Ligand/IonBETA-D-MANNOSE
2CA22Ligand/IonCALCIUM ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FUC1Ligand/IonALPHA-L-FUCOSE
5MAN6Ligand/IonALPHA-D-MANNOSE
6NAG17Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:11 , GLU A:71 , ASP A:102 , ILE A:103 , ASP A:105 , ASP A:138binding site for residue CA A 616
02AC2SOFTWAREGLU A:11 , ASP A:69 , GLU A:71 , ASP A:105 , HOH A:754binding site for residue CA A 617
03AC3SOFTWAREASN A:104 , ASN A:106 , ASP A:136 , ASP A:138 , ASN A:144 , ASP A:194binding site for residue CA A 618
04AC4SOFTWAREGLU A:121 , GLU A:181 , ASP A:215 , VAL A:216 , ASP A:218 , ASP A:250 , CA A:620binding site for residue CA A 619
05AC5SOFTWAREGLU A:121 , ASP A:179 , GLU A:181 , ASP A:218 , ASN A:219 , CA A:619 , HOH A:726binding site for residue CA A 620
06AC6SOFTWAREASN A:217 , ASN A:219 , ASP A:248 , ASP A:250 , ASN A:256 , ASN A:307binding site for residue CA A 621
07AC7SOFTWAREGLU A:350 , GLU A:407 , ASP A:442 , ILE A:443 , ASP A:445 , ASP A:472 , CA A:626binding site for residue CA A 622
08AC8SOFTWAREASN A:444 , ASN A:446 , ASP A:470 , ASP A:472 , ASN A:476 , ASP A:525binding site for residue CA A 623
09AC9SOFTWAREGLU A:234 , GLU A:294 , ASN A:332 , VAL A:333 , GLU A:335 , ASP A:370binding site for residue CA A 624
10AD1SOFTWAREGLU A:234 , ASP A:292 , GLU A:294 , GLU A:335 , GLU A:369 , HOH A:701binding site for residue CA A 625
11AD2SOFTWAREGLU A:350 , ASP A:405 , GLU A:407 , ASP A:445 , CA A:622 , HOH A:718binding site for residue CA A 626
12AD3SOFTWAREARG A:86 , GLY A:87 , THR B:371binding site for residue EDO A 627
13AD4SOFTWAREGLU B:11 , GLU B:71 , ASP B:102 , ILE B:103 , ASP B:105 , ASP B:138binding site for residue CA B 914
14AD5SOFTWAREASN B:104 , ASN B:106 , ASP B:136 , ASP B:138 , ASN B:144 , ASP B:194binding site for residue CA B 915
15AD6SOFTWAREGLU B:121 , GLU B:181 , ASP B:215 , VAL B:216 , ASP B:218 , ASP B:250binding site for residue CA B 916
16AD7SOFTWAREASN B:217 , ASN B:219 , ASP B:248 , ASP B:250 , ASN B:256 , ASN B:307binding site for residue CA B 917
17AD8SOFTWAREGLU B:350 , ASP B:405 , GLU B:407 , ASP B:445 , ASN B:446 , CA B:924 , HOH B:1015binding site for residue CA B 918
18AD9SOFTWAREASN B:444 , ASN B:446 , ASP B:470 , ASP B:472 , ASN B:476 , ASP B:525binding site for residue CA B 919
19AE1SOFTWAREGLU B:121 , ASP B:179 , GLU B:181 , ASP B:218 , HOH B:1014 , HOH B:1025binding site for residue CA B 920
20AE2SOFTWAREGLU B:234 , GLU B:294 , ASN B:332 , VAL B:333 , GLU B:335 , ASP B:370binding site for residue CA B 921
21AE3SOFTWAREGLU B:11 , ASP B:69 , GLU B:71 , ASP B:105 , HOH B:1058binding site for residue CA B 922
22AE4SOFTWAREGLU B:234 , ASP B:292 , GLU B:294 , GLU B:335 , GLU B:369 , HOH B:1002binding site for residue CA B 923
23AE5SOFTWAREGLU B:350 , GLU B:407 , ASP B:442 , ILE B:443 , ASP B:445 , ASP B:472 , CA B:918binding site for residue CA B 924
24AE6SOFTWAREASN A:19 , ASN A:63binding site for Poly-Saccharide residues NAG A 602 through BMA A 604 bound to ASN A 63
25AE7SOFTWAREASN A:133binding site for Poly-Saccharide residues NAG A 605 through BMA A 607 bound to ASN A 133
26AE8SOFTWAREASN A:260 , PHE A:261 , THR A:262binding site for Mono-Saccharide NAG A 608 bound to ASN A 260
27AE9SOFTWAREASN A:413binding site for Mono-Saccharide NAG A 601 bound to ASN A 413
28AF1SOFTWAREARG A:429 , THR A:431 , GLU B:233binding site for Mono-Saccharide MAN A 613 bound to THR A 431
29AF2SOFTWARETHR A:433binding site for Mono-Saccharide MAN A 614 bound to THR A 433
30AF3SOFTWARESER A:342 , LYS A:419 , THR A:433 , THR A:435binding site for Mono-Saccharide MAN A 615 bound to THR A 435
31AF4SOFTWAREASN A:465 , THR A:467 , ARG A:499 , GLU A:501 , SER A:504binding site for Poly-Saccharide residues NAG A 609 through FUC A 612 bound to ASN A 465
32AF5SOFTWAREASN B:19 , PRO B:20 , ASN B:63binding site for Poly-Saccharide residues NAG B 904 through NAG B 905 bound to ASN B 63
33AF6SOFTWAREPHE B:115 , LYS B:131 , ASN B:133binding site for Poly-Saccharide residues NAG B 906 through BMA B 908 bound to ASN B 133
34AF7SOFTWAREASN B:260 , PHE B:261 , THR B:262 , HOH B:1003binding site for Poly-Saccharide residues NAG B 909 through NAG B 910 bound to ASN B 260
35AF8SOFTWAREASN B:413binding site for Mono-Saccharide NAG B 911 bound to ASN B 413
36AF9SOFTWAREASN A:235 , GLN A:236 , VAL A:237 , GLU A:290 , ARG B:429 , THR B:431binding site for Mono-Saccharide MAN B 901 bound to THR B 431
37AG1SOFTWARETHR B:431 , THR B:433binding site for Mono-Saccharide MAN B 902 bound to THR B 433
38AG2SOFTWARESER B:342 , LYS B:419 , THR B:435binding site for Mono-Saccharide MAN B 903 bound to THR B 435
39AG3SOFTWARELYS A:399 , ASN B:465 , GLU B:501 , SER B:504 , LEU B:506binding site for Poly-Saccharide residues NAG B 912 through NAG B 913 bound to ASN B 465

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:447 -A:531
2A:458 -A:544
3A:542 -A:550
4B:447 -B:531
5B:458 -B:544
6B:542 -B:550

(-) Cis Peptide Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1Asn A:19 -Pro A:20
2Pro A:48 -Pro A:49
3Glu A:155 -Pro A:156
4Tyr A:158 -Pro A:159
5Tyr A:427 -Pro A:428
6His A:474 -Pro A:475
7Lys A:487 -Pro A:488
8Asn B:19 -Pro B:20
9Pro B:48 -Pro B:49
10Glu B:155 -Pro B:156
11Tyr B:158 -Pro B:159
12Tyr B:427 -Pro B:428
13His B:474 -Pro B:475
14Lys B:487 -Pro B:488

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERD)

(-) 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:554
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhh.................eeeee...........eee......eee..........eeeeeeeee..........eeeeeeee.......ee...eeeeeee.......eeee..ee............eeeeeeee......eee.....eeee...........eeeeeeeee..............eeeeeee.......ee.....eeeee......eeeeeeee...........eeeeeee......eeeeee....eeeeee.............eeeeeee................eeeeeeee.....ee....eeeeeee..........eeee...ee........eeeeee......eee.....eeee..............eeeeeeeeee......eeeeeeeeeee.......ee...eeeee.....eeeeee....................hhhhheeeeee...eeeeee......eeeeee.............eeeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erd A   1 AWITAPVALREGEDLSKKNPIAKIHSDLAEERGLKITYKYTGKGITEPPFGIFVFNKDTGELNVTSILDREETPFFLLTGYALDARGNNVEKPLELRIKVLDINDNEPVFTQDVFVGSVEELSAAHTLVMKINATDADEPNTLNSKISYRIVSLEPAYPPVFYLNKDTGEIYTTSVTLDREEHSSYTLTVEARDGNGEVTDKPVKQAQVQIRILDVNDNIPVVENKVLEGMVEENQVNVEVTRIKVFDADEIGSDNWLANFTFASGNEGGYFHIETDAQTNEGIVTLIKEVDYEEMKNLDFSVIVANKAAFHKSIRSKYKPTPIPIKVKVKNVKEGIHFKSSVISIYVSESMDRSSKGQIIGNFQAFDEDTGLPAHARYVKLEDRDNWISVDSVTSEIKLAKLPDFESRYVQNGTYTVKIVAISEDYPRKTITGTVLINVEDINDNCPTLIEPVQTICHDAEYVNVTAEDLDGHPNSGPFSFSVIDKPPGMAEKWKIARQESTSVLLQQSEKKLGRSEIQFLISDNQGFSCPEKQVLTLTVCECLHGSGCREAH 554
                                    10        20        30        40        50        60        70        80        90       100       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       550    


Chain B from PDB  Type:PROTEIN  Length:559
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....hhhhh..ee...hhhhhhh...eeeee...........eee.....eeee..........eeeeeeeee..........eeeeeeee.......ee...eeeeeee.......eeee..ee............eeeeeeee......eee.....eeee...........eeeeeeeee............eeeeeeeee.......ee......eeee.....eeeeeeeee...........eeeeeee......eeeeee....eeeeee.............eeeeeee................eee.eeee.....ee....eeeeeee..........eeee...ee........eeeeee......eee.....eeee..............eeeeeeeeee......eeeeeeeeeee.......ee...eeeee.....eeeeee....................hhhhheeeeee...eeeeee......eeeeee.............eeeeeeee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erd B   1 AWITAPVALREGEDLSKKNPIAKIHSDLAEERGLKITYKYTGKGITEPPFGIFVFNKDTGELNVTSILDREETPFFLLTGYALDARGNNVEKPLELRIKVLDINDNEPVFTQDVFVGSVEELSAAHTLVMKINATDADEPNTLNSKISYRIVSLEPAYPPVFYLNKDTGEIYTTSVTLDREEHSSYTLTVEARDGNGEVTDKPVKQAQVQIRILDVNDNIPVVENKVLEGMVEENQVNVEVTRIKVFDADEIGSDNWLANFTFASGNEGGYFHIETDAQTNEGIVTLIKEVDYEEMKNLDFSVIVANKAAFHKSIRSKYKPTPIPIKVKVKNVKEGIHFKSSVISIYVSESMDRSSKGQIIGNFQAFDEDTGLPAHARYVKLEDRDNWISVDSVTSEIKLAKLPDFESRYVQNGTYTVKIVAISEDYPRKTITGTVLINVEDINDNCPTLIEPVQTICHDAEYVNVTAEDLDGHPNSGPFSFSVIDKPPGMAEKWKIARQESTSVLLQQSEKKLGRSEIQFLISDNQGFSCPEKQVLTLTVCECLHGSGCREAHHHHHH 559
                                    10        20        30        40        50        60        70        80        90       100       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       550
   Legend:   → Mismatch (orange background)
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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 5ERD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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        DSG2_HUMAN | Q14126: 2yqg 5j5j

(-) Related Entries Specified in the PDB File

5eqx 5EQX CONTAINS THE ECTODOMAIN OF DESMOGLEIN-3, A RELATED DESMOSOMAL CADHERIN
5erp