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(-) Description

Title :  DECARBOXYLASE CATALYTIC ANTIBODY 21D8-HAPTEN COMPLEX
 
Authors :  K. Hotta, I. A. Wilson
Date :  09 Nov 99  (Deposition) - 11 Oct 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Catalytic Antibody, Chimeric Fab, Decarboxylase, Hapten Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hotta, H. Lange, D. J. Tantillo, K. N. Houk, D. Hilvert, I. A. Wilson
Catalysis Of Decarboxylation By A Preorganized Heterogeneou Microenvironment: Crystal Structures Of Abzyme 21D8.
J. Mol. Biol. V. 302 1213 2000
PubMed-ID: 11183784  |  Reference-DOI: 10.1006/JMBI.2000.4503

(-) Compounds

Molecule 1 - CHIMERIC DECARBOXYLASE ANTIBODY 21D8
    Cell: B-LYMPHOCYTE
    Cell Line: 21D8
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Plasmid: P4XH-M13
    Expression System Strain: TOPP2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FAB
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090,9606
    Other Details: THE CONSTANT DOMAIN (RESIDUES 103-214) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-102) IS FROM MURINE SOURCE
    Strain: BALB/C, BALB/C
 
Molecule 2 - CHIMERIC DECARBOXYLASE ANTIBODY 21D8
    Cell: B-LYMPHOCYTE
    Cell Line: 21D8
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: PERIPLASM
    Expression System Plasmid: P4XH-M13
    Expression System Strain: TOPP2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FAB
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090,9606
    Other Details: THE CONSTANT DOMAIN (RESIDUES 109-230) IS FROM HUMAN SOURCE, AND THE VARIABLE DOMAIN (RESIDUES 1-108) IS FROM MURINE SOURCE
    Strain: BALB/C, BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TK41Ligand/Ion2-ACETYLAMINO-NAPTHALENE-1,5-DISULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , HIS H:35 , ILE H:95 , ALA H:101 , TRP H:103 , SER L:34 , LEU L:36 , ARG L:46 , SER L:67 , ASP L:70 , LEU L:89 , TYR L:91 , ARG L:96 , HOH L:1064 , HOH L:1089BINDING SITE FOR RESIDUE TK4 L 1001
2AC2SOFTWAREPHE H:174 , PRO H:175 , VAL H:177 , SER H:186 , LEU H:187 , SER H:188 , HOH H:2027 , GLN L:160 , SER L:162 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL H 2001
3AC3SOFTWARETHR H:9 , LEU H:11 , LEU H:108 , GLU H:150 , HOH H:2016 , HOH H:2135 , HOH L:1014 , HOH L:1052BINDING SITE FOR RESIDUE GOL H 2002

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Phe L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C5C)

(-) Exons   (0, 0)

(no "Exon" information available for 1C5C)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains d1c5ch1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                  d1c5ch2 H:114-230 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1c5cH01 H:1-113 Immunoglobulins                                                                                 1c5cH02 H:114-227 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee....hhh.eeeeeee..ee...eeeee.......................................eeee...............................hhhhh....eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5c H   1 QVQLLEPGTELVKPGASVKLSCRASGYSFTSYWMHWVKQRPGQGLEWIGLIDPSNGRTNFNDKFKSRATLTVDTSSSTAYMQLSSLTSEDSAVYYCVRIAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 230
                                    10        20        30        40        50  |     59        69        79   |||  86       101       111       121       133       143       153||||   168||     179||     190       200||     213       223|    
                                                                              52A                            82A||           95|                          130|                  154|||    169|      180|               200||               223|    
                                                                                                              82B|           101                           133                   156||     171       182                203|                226    
                                                                                                               82C                                                                157|                                   205                       
                                                                                                                                                                                   162                                                             


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1c5cl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1c5cl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1c5cL01 L:1-108 Immunoglobulins                                                                             1c5cL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee....hhh..eeeeee......ee...eeeee.......eeeee...hhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5c L   1 EIQLTQSPSSLSASLGERVSLTCRTSQEISGYLSWLQQKPDGTIKRLIYDATKLDSGAPKRFSGSRSGSDYSLTISSLESEDFADYYCLQYASFPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    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)
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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  (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 1C5C)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1C5C)

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(-) Related Entries Specified in the PDB File

1c5b DECARBOXYLASE CATALYTIC ANTIBODY 21D8 UNLIGANDED