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(-) Description

Title :  CRYSTAL STRUCTURE OF QUORUM-QUENCHING ANTIBODY 1G9
 
Authors :  R. N. Kirchdoerfer, E. W. Debler, I. A. Wilson
Date :  26 Jan 07  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Antibody, Fab, Induced Fit, Quorum Sensing, Homoserine Lactone, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Debler, G. F. Kaufmann, R. N. Kirchdoerfer, J. M. Mee, K. D. Janda, I. A. Wilson
Crystal Structures Of A Quorum-Quenching Antibody.
J. Mol. Biol. V. 368 1392 2007
PubMed-ID: 17400249  |  Reference-DOI: 10.1016/J.JMB.2007.02.081

(-) Compounds

Molecule 1 - MURINE ANTIBODY FAB RS2-1G9 LAMBDA LIGHT CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: PURIFIED FROM ASCITIC FLUID
    Strain: BALB/C
 
Molecule 2 - MURINE ANTIBODY FAB RS2-1G9 IGG1 HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: PURIFIED FROM ASCITIC FLUID
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS H:35 , ASN H:100 , GLY H:100C , TRP H:100D , PHE H:100E , ASN L:34 , TRP L:96BINDING SITE FOR RESIDUE EDO H 229

(-) 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  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:148 -Pro H:149
3Glu H:150 -Pro H:151
4Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OP4)

(-) Exons   (0, 0)

(no "Exon" information available for 2OP4)

(-) 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 Q5BJZ2_RAT | Q5BJZ2 from UniProtKB/TrEMBL  Length:458

    Alignment length:222
                                                                                                                               119                                                                                                                        
                                                                                                                            118  | 123 124                                                                                                                
                                    29        39        49        59        69        79        89        99       109        |- |   | 124       134       144       154       164       174       184       194       204       214       224       234  
          Q5BJZ2_RAT     20 QVQLQQSGAELVKPGSSVKISCKASGYTFTNYDIHWIKQQPGNGLEWIGWIYPGNGNTKYNQKFNGKATLTADKSSSTAYMQLSSLTSEDSAVYFCARD--YFDGY---DYWGQGVMVTVSSAETTAPSVYPLAPGTALKSNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVPR  236
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2op4H01 H:1-114 Immunoglobulins                                                                                            2op4H02 H:115-     228 Immunoglobulins                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee....-----.eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.hhhhhh..eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2op4 H    1 QVQLQQSGSELVRPGASVKLSCKASGYTFTTYWIHWVKQRPGQGLEWIGTIYPGSDNTYYDEKFKNKATLTVDTSSSTAFMQLSSLTSEDSAVYFCTRGSLYYNNYGWFGYWGQGTLVTVSAAKTTPPSVYPLAPGS-----SMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLTSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121      |  -  |    143       153||||   169       181       191    || 203  ||   214       226  
                                                                              52A                            82A||               100A||||                         128   136               154|||  167|     177|             196| || 206|            223|  
                                                                                                              82B|                100B|||                                                  156||   169      180              198 ||  208             226  
                                                                                                               82C                 100C||                                                   157|                               200|                       
                                                                                                                                    100D|                                                    162                                202                       
                                                                                                                                     100E                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d2op4l1 L:1-108 automated matches                                                                              d2op4l2 L:109-212 automated matches                                                                   SCOP domains
               CATH domains 2op4L01 L:1-107 Immunoglobulins                                                                               2op4L02 L:108-212 Immunoglobulins                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhh...eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2op4 L    1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTRNYANWVQEKPDHFFTGLIGDTNNRAPGVPARFSGSLIGHKAALTITGAQTEDESVYFCALWYSNHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTAGAWERHSSYSCQVTHEGHTVEKSLSRA  212
                                    11        21      ||28        38        48        58        68        78        88        98       107       117       127       137       147       157       167||     178       188       198 ||    210  
                                    9|              27A||                                                                            106A                                                           168|                           200|         
                                    11               27B|                                                                                                                                            170                            203         
                                                      27C
   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  (2, 2)

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 2OP4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2OP4)

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 Related Entries

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UniProtKB/Swiss-Prot
        Q5BJZ2_RAT | Q5BJZ2: 2g60

(-) Related Entries Specified in the PDB File

2ntf CRYSTAL STRUCTURE OF QUORUM-QUENCHING ANTIBODY 1G9 IN COMPLEX WITH AN N-ACYL-L-HOMOSERINE LACTONE ANALOG