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(-) Description

Title :  RETRO-DIELS-ALDERASE CATALYTIC ANTIBODY 9D9
 
Authors :  M. Hugot, J. L. Reymond, U. Baumann
Date :  06 May 02  (Deposition) - 03 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab, Catalytic Antibody, Retro-Deils-Alderase, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hugot, N. Bensel, M. Vogel, M. T. Reymond, B. Stadler, J. L. Reymond, U. Baumann
A Structural Basis For The Activity Of Retro-Diels-Alder Catalytic Antibodies: Evidence For A Catalytic Aromatic Residue.
Proc. Natl. Acad. Sci. Usa V. 99 9674 2002
PubMed-ID: 12093912  |  Reference-DOI: 10.1073/PNAS.142286599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IF KAPPA LIGHT CHAIN
    Chains: L
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: THE ANTIBODIES WERE ISOLATED FROM HYBRIDOMA CELLS AND FAB FRAGMENTS WERE GENERATED BY PAPAIN DIGESTION.
    Synonym: CATALYTIC ANTIBODY 9D9
 
Molecule 2 - IG GAMMA 2A HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: THE ANTIBODIES WERE ISOLATED FROM HYBRIDOMA CELLS AND FAB FRAGMENTS WERE GENERATED BY PAPAIN DIGESTION.

 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 1LO4)

(-) Sites  (0, 0)

(no "Site" information available for 1LO4)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:95
2H:145 -H:200
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:99 -Pro L:100
2Tyr L:145 -Pro L:146
3Phe H:151 -Pro H:152
4Glu H:153 -Pro H:154
5Trp H:193 -Pro H:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LO4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LO4)

(-) Exons   (0, 0)

(no "Exon" information available for 1LO4)

(-) 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
 aligned with Q91Z05_MOUSE | Q91Z05 from UniProtKB/TrEMBL  Length:473

    Alignment length:221
                                                                                                                             118                                                                                                                         
                                                                                                                           117 |                                                                                                                         
                                    29        39        49        59        69        79        89        99       109       118       128       138       148       158       168       178       188       198       208       218       228       238 
         Q91Z05_MOUSE    20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCAR-ELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGP 239
               SCOP domains d1lo4h1 H:1-118 Immunoglobulin heavy chain variable dom ain, VH                                                        d1lo4h2 H:119-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1lo4H01 H:1-118 Immunoglobulins                                                                                        1lo4H02 H:119-217 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee....-.eee........eeeee....eeeeee...hhhhheeeeeeeee...eeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lo4 H   1 ELKLVETGGDLVKPGGSLTLSCEASGFTLRTYGMSWVRQTPQMRLEWVASISYGG-LLYFSDSVKGRFTISRDIVRNILTLQMSRLRSEDTAIYYCARGTSFVRYFDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTQVDKKIVPRAA 220
                                    10        20        30        40        50    | | 59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
                                                                                 55 |                                                                                                                                                                    
                                                                                   56                                                                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:217
 aligned with Q65ZC0_MOUSE | Q65ZC0 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         Q65ZC0_MOUSE     1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRG 217
               SCOP domains d1lo4l1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1lo4l2 L:113-217 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1lo4L01 L:1-113 Immunoglobulins                                                                                  -1lo4L02 L:115-214 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lo4 L   1 DVLLTQTPLSLPVSLGDQASISCRSSQTIVHTNGNTYFEWYLQKPGQSPHLLIYKVSNRLSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYYCFQGSHSPWTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 217
                                    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)
    → 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  (4, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LO4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1LO4)

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  Cis Peptide Bonds
    Glu H:153 - Pro H:154   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Ser L:99 - Pro L:100   [ RasMol ]  
    Trp H:193 - Pro H:194   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
 

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  1lo4
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  Q91Z05_MOUSE | Q91Z05
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q65ZC0_MOUSE | Q65ZC0: 2g60
UniProtKB/TrEMBL
        Q65ZC0_MOUSE | Q65ZC0: 1i9i 1i9j 1l7t 1lo2 1lo3 1t66 2gjz 2gk0
        Q91Z05_MOUSE | Q91Z05: 1i9i 1i9j 1jgu 1jgv 1l7t 1lo2 1lo3 1t66 2gk0

(-) Related Entries Specified in the PDB File

1l00 CATALYTIC RETRO-DIELS-ALDERASE TRANSITION STATE ANALOGUE COMPLEX
1l02 RETRO-DIELS-ALDERASE CATALYTIC ANTIBODY
1l03 RETRO-DIELS-ALDERASE CATALYTIC ANTIBODY