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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN P-CADHERIN (SS-X-DIMER POCKET I)
 
Authors :  J. M. M. Caaveiro, S. Kudo, K. Tsumoto
Date :  04 May 15  (Deposition) - 07 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimerization, Conformational Change, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kudo, J. M. Caaveiro, K. Tsumoto
Adhesive Dimerization Of Human P-Cadherin Catalyzed By A Chaperone-Like Mechanism
Structure V. 24 1523 2016
PubMed-ID: 27545624  |  Reference-DOI: 10.1016/J.STR.2016.07.002

(-) Compounds

Molecule 1 - CADHERIN-3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidCHAMPION PET SUMO
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 108-320
    GeneCDH3, CDHP
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLACENTAL CADHERIN,P-CADHERIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3NI3Ligand/IonNICKEL (II) ION
4SO44Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:102 , HIS A:104 , ASP A:134 , ASP A:136 , ASN A:143 , ASP A:195binding site for residue CA A 301
02AC2SOFTWAREGLU A:11 , GLU A:69 , ASP A:100 , GLN A:101 , ASP A:103 , ASP A:136binding site for residue CA A 302
03AC3SOFTWAREHIS A:104 , SO4 A:305 , SO4 A:306binding site for residue NI A 303
04AC4SOFTWAREMET A:0 , MET B:0 , HOH B:404binding site for residue NI A 304
05AC5SOFTWAREASP A:67 , GLU A:69 , HIS A:104 , GLU A:135 , NI A:303 , SO4 A:306binding site for residue SO4 A 305
06AC6SOFTWAREASP A:67 , ASP A:103 , HIS A:104 , NI A:303 , SO4 A:305binding site for residue SO4 A 306
07AC7SOFTWAREASP A:197 , ASP A:199 , ASN B:12binding site for residue GOL A 307
08AC8SOFTWAREGLU B:11 , GLU B:69 , ASP B:100 , GLN B:101 , ASP B:103 , ASP B:136binding site for residue CA B 301
09AC9SOFTWAREASN B:102 , HIS B:104 , ASP B:134 , ASP B:136 , ASN B:143 , ASP B:195binding site for residue CA B 302
10AD1SOFTWAREHIS B:104 , SO4 B:304 , SO4 B:305 , HOH B:401binding site for residue NI B 303
11AD2SOFTWAREASP B:67 , ASP B:103 , HIS B:104 , NI B:303 , SO4 B:305 , HOH B:401binding site for residue SO4 B 304
12AD3SOFTWAREASP B:67 , HIS B:104 , GLU B:135 , NI B:303 , SO4 B:304 , HOH B:401binding site for residue SO4 B 305
13AD4SOFTWAREASN A:12 , MET B:196 , ASP B:199binding site for residue GOL B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Gly A:15 -Pro A:16
2Phe A:17 -Pro A:18
3Pro A:46 -Pro A:47
4Glu A:154 -Pro A:155
5Asp A:157 -Pro A:158
6Gly B:15 -Pro B:16
7Phe B:17 -Pro B:18
8Pro B:46 -Pro B:47
9Glu B:154 -Pro B:155
10Asp B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZMV)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee........eeeee..hhhhhh..eeeeee...........eee.....eeee..........eeeeeeeeee.........eeeeeeee.......ee...eeeeeee.......eeee..ee.............eeeeeeee........eee.....eeee...........eeeeeeeee.hhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zmv A   0 MDWVIPPISVPENGKGPFPQRLVQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAKYELFGHAVSENGASVEDPMNISIIVTDQNDHKPKFTQDTFRGSVLEGVLPGTSVMQVTATDEDDAIYTYNGVVAYSIHSQEPKDPHDLMFTIHRSTGTISVISSGLDREKVPEYTLTIQATDMDGDGSTTTAVAVVEILD 213
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    

Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee........eeeee..hhhhhh...eeeee...........eee.....eeee..........eeeeeeeee..........eeeeeeee.......ee...eeeeeee.......eeee..ee.............eeeeeeee........eee.....eeee...........eeeeeeeee.hhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zmv B   0 MDWVIPPISVPENGKGPFPQRLVQLKSNKDRDTKIFYSITGPGADSPPEGVFAVEKETGWLLLNKPLDREEIAKYELFGHAVSENGASVEDPMNISIIVTDQNDHKPKFTQDTFRGSVLEGVLPGTSVMQVTATDEDDAIYTYNGVVAYSIHSQEPKDPHDLMFTIHRSTGTISVISSGLDREKVPEYTLTIQATDMDGDGSTTTAVAVVEILD 213
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    

   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 4ZMV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

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
        CADH3_HUMAN | P222234oy9 4zml 4zmn 4zmo 4zmp 4zmq 4zmt 4zmw 4zmx 4zmy 4zmz 5jyl 5jym

(-) Related Entries Specified in the PDB File

4zml 4zmn 4zmo 4zmp 4zmq 4zmt 4zmw 4zmx 4zmy 4zmz