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(-) Description

Title :  ANTIBODIES SPECIFICALLY TARGETING A LOCALLY MISFOLDED REGION OF TUMOR ASSOCIATED EGFR
 
Authors :  T. P. J. Garrett, A. W. Burgess
Date :  05 Feb 09  (Deposition) - 15 Dec 09  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. P. J. Garrett, A. W. Burgess, H. K. Gan, R. B. Luwor, G. Cartwright, F. Walker, S. G. Orchard, A. H. A. Clayton, E. C. Nice, J. Rothacker, B. Catimel, W. K. Cavenee, L. J. Old, E. Stockert, G. Ritter, T. E. Adams P. A. Hoyne, D. Wittrup, G. Chao, J. R. Cochran, C. Luo, M. Lou, T. Huyton Y. Xu, W. D. Fairlie, S. Yao, A. M. Scott, T. G. Johns
Antibodies Specifically Targeting A Locally Misfolded Regio Of Tumor Associated Egfr
Proc. Natl. Acad. Sci. Usa V. 106 5082 2009
PubMed-ID: 19289842  |  Reference-DOI: 10.1073/PNAS.0811559106

(-) Compounds

Molecule 1 - 806 LIGHT CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA CELL
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 806 HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA CELL
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3G5X)

(-) Sites  (0, 0)

(no "Site" information available for 3G5X)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:129
4B:22 -B:94
5B:141 -B:196
6C:23 -C:88
7C:134 -C:194
8C:214 -D:129
9D:22 -D:94
10D:141 -D:196

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Phe A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:147 -Pro B:148
5Trp B:189 -Pro B:190
6Ser C:7 -Pro C:8
7Phe C:94 -Pro C:95
8Tyr C:140 -Pro C:141
9Phe D:147 -Pro D:148
10Trp D:189 -Pro D:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G5X)

(-) Exons   (0, 0)

(no "Exon" information available for 3G5X)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains d3g5xa1 A:1-107 automated matches                                                                          d3g5xa2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------3g5xA02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee.....hhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5x A   1 DILMTQSPSSMSVSLGDTVSITCHSSQDINSNIGWLQQKPGKSFKGLIYHGTNLDDEVPSRFSGSGSGADYSLTISSLESEDFADYYCVQYAQFPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3g5xB01 B:1-114 Immunoglobulins                                                                                     3g5xB02 B:115-213 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g5x B   1 DVQLQESGPSLVKPSQSLSLTCTVTGYSITSDFAWNWIRQFPGNKLEWMGYISYSGNTRYNPSLKSRISITRDTSKNQFFLQLNSVTIEDTATYYCVTAGRGFPYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEPS 214
                                    10        20        30        40        50        60        70        80  ||||  88        98       108       118       128       138       148       158       168       178       188       198       208      
                                                                                                             83|||                                                                                                                                  
                                                                                                             583||                                                                                                                                  
                                                                                                              584|                                                                                                                                  
                                                                                                                84                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d3g5xc1 C:1-107 automated matches                                                                          d3g5xc2 C:108-214 automated matches                                                                         SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------3g5xC02 C:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee.....hhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5x C   1 DILMTQSPSSMSVSLGDTVSITCHSSQDINSNIGWLQQKPGKSFKGLIYHGTNLDDEVPSRFSGSGSGADYSLTISSLESEDFADYYCVQYAQFPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3g5xD01 D:1-114 Immunoglobulins                                                                                     3g5xD02 D:115-213 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeeee........eeeee..........eeeeeeeeeee.....eeee.........ee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g5x D   1 DVQLQESGPSLVKPSQSLSLTCTVTGYSITSDFAWNWIRQFPGNKLEWMGYISYSGNTRYNPSLKSRISITRDTSKNQFFLQLNSVTIEDTATYYCVTAGRGFPYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEPS 214
                                    10        20        30        40        50        60        70        80  ||||  88        98       108       118       128       138       148       158       168       178       188       198       208      
                                                                                                             83|||                                                                                                                                  
                                                                                                             583||                                                                                                                                  
                                                                                                              584|                                                                                                                                  
                                                                                                                84
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Mouse (Mus musculus) (152)
1a3g5xA02A:108-211
1b3g5xC02C:108-211
1c3g5xB02B:115-213
1d3g5xD02D:115-213
1e3g5xB01B:1-114
1f3g5xD01D:1-114

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G5X)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3G5X)

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  Cis Peptide Bonds
    Phe A:94 - Pro A:95   [ RasMol ]  
    Phe B:147 - Pro B:148   [ RasMol ]  
    Phe C:94 - Pro C:95   [ RasMol ]  
    Phe D:147 - Pro D:148   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
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    Trp B:189 - Pro B:190   [ RasMol ]  
    Trp D:189 - Pro D:190   [ RasMol ]  
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    Tyr C:140 - Pro C:141   [ RasMol ]  
 
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