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 EPIREGULIN IN COMPLEX WITH THE FAB FRAGMENT OF MURINE MONOCLONAL ANTIBODY 9E5
 
Authors :  Y. Kado, E. Mizohata, S. Nagatoishi, M. Iijima, K. Shinoda, T. Miyafusa T. Nakayama, T. Yoshizumi, A. Sugiyama, T. Kawamura, Y. H. Lee, H. Mats H. Doi, H. Fujitani, T. Kodama, Y. Shibasaki, K. Tsumoto, T. Inoue
Date :  14 Oct 15  (Deposition) - 09 Dec 15  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Antibody, Immunoglobulin, Monoclonal Antibody, Epidermal Growth Factor, Cancer, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kado, E. Mizohata, S. Nagatoishi, M. Iijima, K. Shinoda, T. Miyafusa, T. Nakayama, T. Yoshizumi, A. Sugiyama, T. Kawamura, Y. H. Lee, H. Matsumura, H. Doi, H. Fujitani, T. Kodama, Y. Shibasaki, K. Tsumoto, T. Inoue
Epiregulin Recognition Mechanisms By Anti-Epiregulin Antibody 9E5: Structural, Functional, And Molecular Dynamic Simulation Analyses
J. Biol. Chem. V. 291 2319 2016
PubMed-ID: 26627827  |  Reference-DOI: 10.1074/JBC.M115.656009

(-) Compounds

Molecule 1 - PROEPIREGULIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EREG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ANTI-HUMAN EPIREGULIN ANTIBODY 9E5 FAB HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - ANTI-HUMAN EPIREGULIN ANTIBODY 9E5 FAB LIGHT CHAIN
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU H:175binding site for residue CL H 301
2AC2SOFTWAREPRO H:124 , VAL H:126 , LYS H:213binding site for residue GOL H 302
3AC3SOFTWAREPHE H:171 , PRO H:172 , THR H:181 , LEU H:182 , SER H:183 , LEU L:159 , SER L:175 , SER L:176 , THR L:177binding site for residue GOL L 301

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:19
2A:14 -A:30
3A:32 -A:41
4H:22 -H:96
5H:145 -H:200
6L:23 -L:88
7L:133 -L:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Phe H:151 -Pro H:152
2Glu H:153 -Pro H:154
3Trp H:193 -Pro H:194
4Ser L:7 -Pro L:8
5Tyr L:139 -Pro L:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E8D)

(-) Exons   (0, 0)

(no "Exon" information available for 5E8D)

(-) 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:43
                                                                           
               SCOP domains ------------------------------------------- SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhh.....eeeeee....eeeeee...ee.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 5e8d A   3 ITKCSSDMNGYCLHGQCIYLVDMSQNYCRCEVGYTGVRCEHFF  45
                                    12        22        32        42   


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.............eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e8d H   1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPLNDKTKYDPKFQGKATITADTSSNSAYLQLSSLTSEDTAVYYCSRGGGDPVFVYWGQGTLVTVSAAKTTPPSVYPLAPGSTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   143       153       163       173       183       193       203       213      
                                                                                                                                                              133|                                                                                  
                                                                                                                                                               137                                                                                  


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....ee......eeeeee.......eeeeee......eeee................eee..eeeee..........eeeeee.....ee...eee.........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e8d L   1 DIQMTQSPSSLSASGKVTITCKASQDINKYIAWYQHKPGKGPRLLIHYTSTLHPGIPSRFSGSGSGRDYSFSISNLEPEDIATYYCLQYDNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 212
                                    10   ||   22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
                                        14|                                                                                                                                                                                                   
                                         17
   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 5E8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E8D)

(-) Gene Ontology  (57, 57)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu H:153 - Pro H:154   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:193 - Pro H:194   [ RasMol ]  
    Tyr L:139 - Pro L:140   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5e8d
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EREG_HUMAN | O14944
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EREG_HUMAN | O14944
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EREG_HUMAN | O14944: 1k36 1k37

(-) Related Entries Specified in the PDB File

5az2