Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN E-CADHERIN (RESIDUES 3-213) IN COMPLEX WITH A PEPTIDOMIMETIC INHIBITOR
 
Authors :  V. Nardone, A. P. Lucarelli, A. Dalle Vedove, E. Parisini
Date :  14 May 15  (Deposition) - 01 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Adhesion, Cadherin, Calcium-Binding Protein, X-Dimer, Inhibitor, Peptidomimetic, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Nardone, A. P. Lucarelli, A. Dalle Vedove, R. Fanelli, A. Tomassetti, L. Belvisi, M. Civera, E. Parisini
Crystal Structure Of Human E-Cadherin-Ec1Ec2 In Complex Wit A Peptidomimetic Competitive Inhibitor Of Cadherin Homophilic Interaction.
J. Med. Chem. V. 59 5089 2016
PubMed-ID: 27120112  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01487

(-) Compounds

Molecule 1 - CADHERIN-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET3A
    Expression System Taxid469008
    Expression System VariantPLYSS
    Expression System Vector TypePLASMID
    FragmentRESIDUES 157-367
    GeneCDH1, CDHE, UVO
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCAM 120/80,EPITHELIAL CADHERIN,E-CADHERIN,UVOMORULIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
14RL2Ligand/IonN-{[(2S,5S)-1-BENZYL-5-(2-{[(2S,3S)-1-(TERT-BUTYLAMINO)-3-METHYL-1-OXOPENTAN-2-YL]AMINO}-2-OXOETHYL)-3,6-DIOXOPIPERAZIN-2-YL]METHYL}-L-ALPHA-ASPARAGINE
2CA6Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:143 , ASP A:195binding site for residue CA A 401
2AC2SOFTWAREGLU A:11 , GLU A:69 , ASP A:100 , GLN A:101 , ASP A:103 , ASP A:136binding site for residue CA A 402
3AC3SOFTWAREGLU A:11 , ASP A:67 , GLU A:69 , ASP A:103 , HOH A:579 , HOH A:610binding site for residue CA A 403
4AC4SOFTWAREASN B:102 , ASN B:104 , ASP B:134 , ASP B:136 , ASN B:143 , ASP B:195binding site for residue CA B 401
5AC5SOFTWAREGLU B:11 , GLU B:69 , ASP B:100 , GLN B:101 , ASP B:103 , ASP B:136binding site for residue CA B 402
6AC6SOFTWAREGLU B:11 , ASP B:67 , GLU B:69 , ASP B:103 , HOH B:511 , HOH B:574binding site for residue CA B 403

(-) SS Bonds  (0, 0)

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

(-) 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
4Asp A:154 -Pro A:155
5Leu A:157 -Pro A:158
6Gly B:15 -Pro B:16
7Phe B:17 -Pro B:18
8Pro B:46 -Pro B:47
9Asp B:154 -Pro B:155
10Leu B:157 -Pro B:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZTE)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee........eeeee..hhhhh...eeeeee...........eee.....eeee..........eeeeeeeeee.........eeeeeeee.......ee...eeeeeee......eeeee..ee.............eeeeeeee........eee.....eeee...........eeeeeeeee.hhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zte A   4 IPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD 213
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213

Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee........eeeee..hhhhh...eeeeeee..........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
                 4zte B   4 IPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD 213
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213

   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 4ZTE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    4RL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:154 - Pro A:155   [ RasMol ]  
    Asp B:154 - Pro B:155   [ RasMol ]  
    Gly A:15 - Pro A:16   [ RasMol ]  
    Gly B:15 - Pro B:16   [ RasMol ]  
    Leu A:157 - Pro A:158   [ RasMol ]  
    Leu B:157 - Pro B:158   [ RasMol ]  
    Phe A:17 - Pro A:18   [ RasMol ]  
    Phe B:17 - Pro B:18   [ RasMol ]  
    Pro A:46 - Pro A:47   [ RasMol ]  
    Pro B:46 - Pro B:47   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4zte
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CADH1_HUMAN | P12830
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CADH1_HUMAN | P12830
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CADH1_HUMAN | P128301o6s 2o72 2omt 2omu 2omv 2omx 2omy 2omz 3ff7 3ff8 3l6x 3l6y 4zt1

(-) Related Entries Specified in the PDB File

4zt1 4ZT1 CONTAINS THE SAME PROTEIN WITHOUT INHIBITOR