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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF MONOCLONAL ANTIBODY 3F8 FAB FRAGMENT THAT BINDS TO GD2 GANGLIOSIDE
 
Authors :  M. Ahmed, Y. Goldgur, N. -K. Cheung
Date :  09 Jan 12  (Deposition) - 06 Feb 13  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Antibody, Gd2 Ganglioside, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ahmed, Y. Goldgur, J. Hu, H. F. Guo, N. K. Cheung
In Silico Driven Redesign Of A Clinically Relevant Antibody For The Treatment Of Gd2 Positive Tumors.
Plos One V. 8 63359 2013
PubMed-ID: 23696816  |  Reference-DOI: 10.1371/JOURNAL.PONE.0063359

(-) Compounds

Molecule 1 - 3F8 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 3F8 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Taxid: 10090
    Organism Common: MOUSE
    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 3VFG)

(-) Sites  (0, 0)

(no "Site" information available for 3VFG)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:92 -H:22
2H:128 -L:214
3H:195 -H:140
4L:88 -L:23
5L:194 -L:134

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VFG)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3vfg H    1 QVQLKESGPGLVAPSQSLSITCTVSGFSVTNYGVHWVRQPPGKGLEWLGVIWAGGITNYNSAFMSRLSISKDNSKSQVFLKMNSLQIDDTAMYYCASRGGHYGYALDYWGQGTSVTVSSASTKGPSVYPLVPGCTSGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR  213
                                    10        20        30        40        50        60        70        80  |||   87        97   ||| 104       114       124   ||  136       146       156       166       176       186       196       206       
                                                                                                            82A||               100A||                         128|                                                                                  
                                                                                                             82B|                100B|                          131                                                                                  
                                                                                                              82C                 100C                                                                                                               


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d3vfgl1 L:1-107 automated matches                                                                       d3vfgl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee........eeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeee.........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3vfg L    1 SIVMTQTPKFLLVSAGDRVTITCKASQSVSNDVTWYQQKAGQSPKLLIYSASNRYSGVPDRFTGSGYGTAFTFTISTVQAEDLAVYFCQQDYSSFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90 ||    103       113       123       133       143       153       163       173       183       193       203       213 
                                                                                                                      92|                                                                                                                      
                                                                                                                       96
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VFG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 3vfg)
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  3vfg
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1psk 2aju