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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF 9E5, A MURINE MONOCLONAL ANTIBODY SPECIFIC FOR HUMAN EPIREGULIN
 
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 :  16 Sep 15  (Deposition) - 09 Dec 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Antibody, Immunoglobulin, Monoclonal Antibody, Epidermal Growth Factor, 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 - ANTI-HUMAN EPIREGULIN ANTIBODY 9E5 FAB HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTI-HUMAN EPIREGULIN ANTIBODY 9E5 FAB LIGHT CHAIN
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5AZ2)

(-) Sites  (0, 0)

(no "Site" information available for 5AZ2)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:145 -H:200
3L:23 -L:88
4L:133 -L:193

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp H:102 -Pro H:103
2Phe H:151 -Pro H:152
3Glu H:153 -Pro H:154
4Trp H:193 -Pro H:194
5Ser L:7 -Pro L:8
6Tyr L:139 -Pro L:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5AZ2)

(-) 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 H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee.............eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5az2 H   1 EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPLNDKTKYDPKFQGKATITADTSSNSAYLQLSSLTSEDTAVYYCSRGGGDPVFVYWGQGTLVTVSAAKTTPPSVYPLAPGSAANSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGC 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 142       152       162       172       182       192       202       212       222
                                                                                                                                                                135|                                                                                    
                                                                                                                                                                 138                                                                                    


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5az2 L   1 DIQMTQSPSSLSASLGGKVTITCKASQDINKYIAWYQHKPGKGPRLLIHYTSTLHPGIPSRFSGSGSGRDYSFSISNLEPEDIATYYCLQYDNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 213
                                    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)
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  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 5AZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AZ2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5AZ2)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 5az2)
 
  Cis Peptide Bonds
    Asp H:102 - Pro H:103   [ RasMol ]  
    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 ]  
 

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