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(-) Description

Title :  STRUCTURE AND SPECIFICITY OF THE ANTI-DIGOXIN ANTIBODY 40-50
 
Authors :  P. D. Jeffrey, S. Sheriff
Date :  25 Oct 94  (Deposition) - 08 May 95  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  H,L  (2x)
Keywords :  Immunoglobulin, Fab, Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. D. Jeffrey, J. F. Schildbach, C. Y. Chang, P. H. Kussie, M. N. Margolies, S. Sheriff
Structure And Specificity Of The Anti-Digoxin Antibody 40-5
J. Mol. Biol. V. 248 344 1995
PubMed-ID: 7739045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2B-KAPPA 40-50 FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: A/J
 
Molecule 2 - IGG2B-KAPPA 40-50 FAB (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : HL
Biological Unit 1 (1x): HL
Biological Unit 2 (2x): HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CU1Ligand/IonCOPPER (II) ION
2OBN1Ligand/IonOUABAIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2OBN1Ligand/IonOUABAIN
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2OBN2Ligand/IonOUABAIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS L:189BINDING SITE FOR RESIDUE CU L 1
2AC2SOFTWAREHIS H:35 , LEU H:50 , PHE H:95 , TYR H:100 , TYR H:100C , VAL H:100E , THR L:27D , HIS L:32 , SER L:91 , ARG L:92 , TYR L:94 , LEU L:96BINDING SITE FOR RESIDUE OBN H 1

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2His L:76 -Pro L:77
3Tyr L:94 -Pro L:95
4Tyr L:140 -Pro L:141
5Phe H:148 -Pro H:149
6Glu H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IBG)

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1ibgh1 H:2-113 Immunoglobulin heavy chain variable domain, VH                                                          d1ibgh2 H:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 1ibgH01 H:2-114 Immunoglobulins                                                                                          1ibgH02 H:115-223 Immunoglobulins                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee....eeeeeeee........eeeeeee.....eeeeeee.....eee...hhhheeeeeehhh.eeeeeee...hhh.eeeeeeee...........eeeeeeeeee........eeeeee.........eeeeeeeeeee.....eeeehhh.....eeee........eeeeeeeeee.........eeeeeehhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ibg H    2 VHLVQSGPGLVAPSQSLSITCTVSGFSLTTYGVHWFRQPPGKGLEWLGLIWAGGNTDYNSALMSRLSINKDNSKSQVFLKMNSLQADDTAMYYCARFRFASYYDYAVDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPEPVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKL  223
                                    11        21        31        41        51        61        71        81 |||    88        98  |||||103       113       123      |135       145       156||     171       183       193  || ||205||     216       
                                                                                                           82A||               100A||||                           130|                  154|||    169|      180|          196| || 206|               
                                                                                                            82B|                100B|||                            133                   156||     171       183           198 ||  208               
                                                                                                             82C                 100C||                                                   157|                               200|                    
                                                                                                                                  100D|                                                    162                                202                    
                                                                                                                                   100E                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1ibgl1 L:2-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                    d1ibgl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1ibgL01 L:2-108 Immunoglobulins                                                                                1ibgL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee...........eeeeeee.....eeeeehhh.........eeeeee..eeeeee....hhh.eeeeeee............eeeee......eeeee...hhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ibg L    2 IVLTQSPASLAVSLGQRATISCRASKSVSTSGYSHIHWYQQKPGQPPKLLIYLASILESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCQHSREYPLTFGAGTELELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    11        21      |27D        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       
                                                    27A|||                                                                                                                                                                                           
                                                     27B||                                                                                                                                                                                           
                                                      27C|                                                                                                                                                                                           
                                                       27D
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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