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(-) Description

Title :  STRUCTURE OF THE ANTI-CHOLERA TOXIN ANTIBODY FAB FRAGMENT TE33 IN COMPLEX WITH A D-PEPTIDE
 
Authors :  P. Scheerer, N. Krauss, H. Wessner, C. Scholz, L. Otte, M. Seifert, A. Kramer, J. Schneider-Mergener, W. Hoehne
Date :  18 Apr 05  (Deposition) - 04 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Polyspecificity, Cross-Reactivity, Anti-Cholera Toxin, Antigen-Antibody Complex, Antigen Recognition, Substitution Matrix, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Scheerer, A. Kramer, L. Otte, M. Seifert, H. Wessner, C. Scholz, N. Krauss, J. Schneider-Mergener, W. Hohne
Structure Of An Anti-Cholera Toxin Antibody Fab In Complex With An Epitope-Derived D-Peptide: A Case Of Polyspecific Recognition.
J. Mol. Recognit. V. 20 263 2007
PubMed-ID: 17712773  |  Reference-DOI: 10.1002/JMR.838
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MONOCLONAL ANTI-CHOLERA TOXIN IGG1 KAPPA ANTIBODY, L CHAIN
    Cell Line: HYBRIDOMA
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - MONOCLONAL ANTI-CHOLERA TOXIN IGG1 KAPPA ANTIBODY, H CHAIN
    Cell Line: HYBRIDOMA
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 3 - SHORT SYNTHETIC D-AMINO ACID PEPTIDE D2
    Chains: A
    Engineered: YES
    Other Details: THIS D-AMINO ACID SEQUENCE OCCURS PEPTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 10)

Asymmetric/Biological Unit (8, 10)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2DAS1Mod. Amino AcidD-ASPARTIC ACID
3DGN1Mod. Amino AcidD-GLUTAMINE
4DHI1Mod. Amino AcidD-HISTIDINE
5DPR1Mod. Amino AcidD-PROLINE
6DSN2Mod. Amino AcidD-SERINE
7DTY1Mod. Amino AcidD-TYROSINE
8DVA1Mod. Amino AcidD-VALINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:100A , TYR L:49 , LYS L:50 , ASN L:53 , HOH L:1097BINDING SITE FOR RESIDUE CIT L 1001
2AC2SOFTWAREDHI A:6 , HOH A:136 , SER L:27E , SER L:92 , HIS L:93 , ILE L:94 , HOH L:1025BINDING SITE FOR RESIDUE CIT L 1002

(-) 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  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZEA)

(-) 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 A from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                1zea A    1 xxGxxxxxx    9
                            || ||||||
                            1-DVA||||
                             2-DPR|||
                               4-DSN|
                                5-DGN
                                 6-DHI
                                  7-DTY
                                   8-DAS
                                    9-DSN


Chain H from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zeaH01 H:1-113 Immunoglobulins                                                                                     1zeaH02 H:114-212 Immunoglobulins                                                           - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.....ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zea H    1 QIQLVQSGPELKTPGETVRISCKASGYTFTTYGMSWVKQTPGKGFKWMGWINTYSGVPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCARRSWYFDVWGTGTTVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96|||    107       117       134       144       154       164       174       184       194       204         
                                                                              52A                            82A||            96|||                       126|                                                                               
                                                                                                              82B|           100A||                        134                                                                               
                                                                                                               82C            100B|                                                                                                          
                                                                                                                               100C                                                                                                          


Chain L from PDB  Type:PROTEIN  Length:216
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
        A2NHM3_MOUSE      1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1zeaL01 L:1-108 Immunoglobulins                                                                                  1zeaL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...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
                1zea L    1 DVLMTQTPLSLPVSLGDQASISCKSSQSIVHSSGNTYFEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHIPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
                                                     27A||||                                                                                                                                                                                        
                                                      27B|||                                                                                                                                                                                        
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 1ZEA)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Q921A6_MOUSE | Q921A6
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 2a1w 2dqt 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe
        Q921A6_MOUSE | Q921A6: 1n4x

(-) Related Entries Specified in the PDB File

1tet THE SAME ANTIBODY FAB FRAGMENT TE33 IN COMPLEX WITH ITS EPITOPE PEPTIDE CTP3