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(-) Description

Title :  STRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC ANTIBODY 1D4
 
Authors :  N. A. Larsen, A. Heine, L. Crane, B. F. Cravatt, R. A. Lerner, I. A. Wilson
Date :  26 Jun 01  (Deposition) - 05 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Igg Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. A. Larsen, A. Heine, L. Crane, B. F. Cravatt, R. A. Lerner, I. A. Wilson
Structural Basis For A Disfavored Elimination Reaction In Catalytic Antibody 1D4.
J. Mol. Biol. V. 314 93 2001
PubMed-ID: 11724535  |  Reference-DOI: 10.1006/JMBI.2001.5112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTIBODY LIGHT CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: PURIFIED FROM ASCITES FLUID
    Strain: BALBC
 
Molecule 2 - ANTIBODY HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: PURIFIED FROM ASCITES FLUID
    Strain: BALBC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HBC1Ligand/Ion(2-AMINO-3-PHENYL-BICYCLO[2.2.1]HEPT-2-YL)-PHENYL-METHANONE
2OH1Ligand/IonHYDROXIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG H:56 , HIS H:58 , HBC H:3001BINDING SITE FOR RESIDUE OH H 4000
2AC2SOFTWARESER H:50 , TYR H:52 , HIS H:58 , ALA H:97 , ARG H:100 , OH H:4000 , HOH H:4076 , VAL L:94 , PRO L:95 , LEU L:96BINDING SITE FOR RESIDUE HBC H 3001

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:94 -Pro L:95
3Pro L:95 -Pro L:95A
4Tyr L:140 -Pro L:141
5Phe H:146 -Pro H:147
6Glu H:148 -Pro H:149
7Trp H:188 -Pro H:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JGU)

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

    Alignment length:218
                                                                                                                             118                                                                                                                      
                                                                                                                           117 |                                                                                                                      
                                    29        39        49        59        69        79        89        99       109       118       128       138       148       158       168       178       188       198       208       218       228        
        Q91Z05_MOUSE     20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCAR-ELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP  236
               SCOP domains d1jguh1 H:1-113 Immunoglobulin heavy chain variable do main, VH                                                        d1jguh2 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1jguH01 H:1-113 Immunoglobulins                                                                                        1jguH02 H:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains V-set-1jguH02 H:1-111                                 -                                                              --------------C1-set-1jguH01 H:126-207                                                          ----- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee......eeeeeeee.....eeeeeeee..-.eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jgu H    1 EVKLVESRGGLVKPGGSLQLSCAASGFTFSGYAMSWFRLTPEKRLEWVASIYNG-FRIHYLDSVKGRFTISSDYARNILYLQMSTLRSEDTAMYYCSRGDAYSRYFDVWGAGTTVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  212
                                    10        20        30        40        50   | |  59        69        79   |||  86        96    || 104       114       124       134       144       154       164       174       184       194       204        
                                                                                54 |                         82A||               100A|                                                                                                                
                                                                                  55                          82B|                100B                                                                                                                
                                                                                                               82C                                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:220
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:221
                                                                                                                                122                                                                                                                      
                                                                                                                              121 |                                                                                                                      
                                    30        40        50        60        70        80        90       100       110       120| |    129       139       149       159       169       179       189       199       209       219       229       239 
        Q52L64_MOUSE     21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYP-LTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  240
               SCOP domains d1jgul1 L:1-107 Immunoglobulin l ight chain kappa variable domain, VL-kappa                                       d1jgul2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1jguL01 L:1-108 Immunoglobulins                                                                                    -1jguL02 L:110-209 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......-.....eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jgu L    1 EVVMTQSPLSLPVSLGDQASISCRSSQSLVHS-NGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|| |    34        44        54        64        74        84        94 |     103       113       123       133       143       153       163       173       183       193       203       213 
                                                     27A|||| |                                                                 95A                                                                                                                       
                                                      27B||| |                                                                                                                                                                                           
                                                       27C|| |                                                                                                                                                                                           
                                                        27D| |                                                                                                                                                                                           
                                                         27E |                                                                                                                                                                                           
                                                            28
   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  (4, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q91Z05_MOUSE | Q91Z05)

Chain L   (Q52L64_MOUSE | Q52L64)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  1jgu
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  Q91Z05_MOUSE | Q91Z05
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 Related Entries

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

UniProtKB/TrEMBL
        Q52L64_MOUSE | Q52L64: 1a3r 1bbd 1h3p 1jgv 1q9w 2fd6 2r1w 2r1x 2r1y 2r23 2r2b 2r2h 3t77
        Q91Z05_MOUSE | Q91Z05: 1i9i 1i9j 1jgv 1l7t 1lo2 1lo3 1lo4 1t66 2gk0

(-) Related Entries Specified in the PDB File

1jgv STRUCTURAL BASIS FOR DISFAVORED ELIMINATION REACTION IN CATALYTIC ANTIBODY 1D4