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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE N-CADHERIN EC1-2 A78SI92M
 
Authors :  X. Jin
Date :  03 Dec 13  (Deposition) - 24 Sep 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cell Adhesion Molecule, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vendome, K. Felsovalyi, H. Song, Z. Yang, X. Jin, J. Brasch, O. J. Harrison, G. Ahlsen, F. Bahna, A. Kaczynska, P. S. Katsamba, D. Edmond, W. L. Hubbell, L. Shapiro, B. Honig
Structural And Energetic Determinants Of Adhesive Binding Specificity In Type I Cadherins.
Proc. Natl. Acad. Sci. Usa V. 111 E4175 2014
PubMed-ID: 25253890  |  Reference-DOI: 10.1073/PNAS.1416737111

(-) Compounds

Molecule 1 - CADHERIN-2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 160-374
    Gene: CDH2
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: NEURAL CADHERIN, N-CADHERIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:142 , ASP A:194BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREGLU A:11 , GLU A:69 , ASP A:100 , MET A:101 , ASP A:103 , ASP A:136BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREGLU A:11 , ASP A:67 , GLU A:69 , ASP A:103BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASN B:102 , ASN B:104 , ASP B:134 , ASP B:136 , ASN B:142 , ASP B:194BINDING SITE FOR RESIDUE CA B 301
05AC5SOFTWAREGLU B:11 , GLU B:69 , ASP B:100 , MET B:101 , ASP B:103 , ASP B:136BINDING SITE FOR RESIDUE CA B 302
06AC6SOFTWAREGLU B:11 , ASN B:12 , ASP B:67 , GLU B:69 , ASP B:103BINDING SITE FOR RESIDUE CA B 303
07AC7SOFTWAREASN C:102 , ASN C:104 , ASP C:134 , ASP C:136 , ASN C:142 , ASP C:194BINDING SITE FOR RESIDUE CA C 301
08AC8SOFTWAREGLU C:11 , GLU C:69 , ASP C:100 , MET C:101 , ASP C:103 , ASP C:136BINDING SITE FOR RESIDUE CA C 302
09AC9SOFTWAREGLU C:11 , ASP C:67 , GLU C:69 , ASP C:103BINDING SITE FOR RESIDUE CA C 303
10BC1SOFTWAREASN D:102 , ASN D:104 , ASP D:134 , ASP D:136 , ASN D:142 , ASP D:194BINDING SITE FOR RESIDUE CA D 301
11BC2SOFTWAREGLU D:11 , GLU D:69 , ASP D:100 , MET D:101 , ASP D:103 , ASP D:136BINDING SITE FOR RESIDUE CA D 302
12BC3SOFTWAREGLU D:11 , ASP D:67 , GLU D:69 , ASP D:103BINDING SITE FOR RESIDUE CA D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NUM)

(-) Cis Peptide Bonds  (20, 20)

Asymmetric Unit
No.Residues
1Gly A:15 -Pro A:16
2Phe A:17 -Pro A:18
3Pro A:46 -Pro A:47
4Ala A:153 -Pro A:154
5Thr A:156 -Pro A:157
6Gly B:15 -Pro B:16
7Phe B:17 -Pro B:18
8Pro B:46 -Pro B:47
9Ala B:153 -Pro B:154
10Thr B:156 -Pro B:157
11Gly C:15 -Pro C:16
12Phe C:17 -Pro C:18
13Pro C:46 -Pro C:47
14Ala C:153 -Pro C:154
15Thr C:156 -Pro C:157
16Gly D:15 -Pro D:16
17Phe D:17 -Pro D:18
18Pro D:46 -Pro D:47
19Ala D:153 -Pro D:154
20Thr D:156 -Pro D:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NUM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NUM)

(-) Exons   (0, 0)

(no "Exon" information available for 4NUM)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeee........eeeee.ee.hhhh...eeeee...........eee.....eeee..........eeeeeeeee..........eeeeeeee.......ee...eeeeeee.......eeee..ee......hhhh.eeeeeeeee........eee.....eeee...........eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4num A   1 DWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRSHAVDINGNQVENPMDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQQYTLIIQATDMEGNPTYGLSNTATAVITVTD 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeee........eeeee.ee.......eeeeee...........eee.....eeee..........eeeeeeeeee.........eeeeeeee.......ee...eeeeeee.......eeee..ee......hhhh.ee..eee..........eee.....eeee...........eeeeeeeeee.........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4num B   1 DWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRSHAVDINGNQVENPMDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQQYTLIIQATDMEGNPTYGLSNTATAVITVTD 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeee........eeeee..hhhhhh...eeeee...........eee.....eeee..........eeeeeeeee..........eeeeeeee.......ee...eeeeeee.......eeee..ee......hhhhh....eee..........eee.....eeee...........eeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4num C   1 DWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRSHAVDINGNQVENPMDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQQYTLIIQATDMEGNPTYGLSNTATAVITVTD 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..........eeeee.ee.hhhh..eeeeee...........eee.....eeee..........eeeeeeeeee.........eeeeee.........ee...eeeeeee.......eeee..ee......hhhhh.eeeeeeee........eee.....eeee...........eeeeeeeee..........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4num D   1 DWVIPPINLPENSRGPFPQELVRIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRSHAVDINGNQVENPMDIVINVIDMNDNRPEFLHQVWNGSVPEGSKPGTYVMTVTAIDADDPNALNGMLRYRILSQAPSTPSPNMFTINNETGDIITVAAGLDREKVQQYTLIIQATDMEGNPTYGLSNTATAVITVTD 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4NUM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NUM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NUM)

(-) Gene Ontology  (61, 61)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        CADH2_MOUSE | P15116: 1ncg 1nch 1nci 1ncj 1op4 2qvi 3q2w 4nup 4nuq

(-) Related Entries Specified in the PDB File

4nup 4nuq