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(-) Description

Title :  STRUCTURAL BASIS FOR LIGAND RECOGNITION AND DISCRIMINATION OF A QUORUM QUENCHING ANTIBODY
 
Authors :  R. K. Kirchdoerfer, G. F. Kaufmann, J. D. Janda, I. A. Wilson
Date :  24 Jan 11  (Deposition) - 23 Mar 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin Fold, Antigen Recognition, Aip4, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. N. Kirchdoerfer, A. L. Garner, C. E. Flack, J. M. Mee, A. R. Horswill, K. D. Janda, G. F. Kaufmann, I. A. Wilson
Structural Basis For Ligand Recognition And Discrimination Of A Quorum-Quenching Antibody.
J. Biol. Chem. V. 286 17351 2011
PubMed-ID: 21454495  |  Reference-DOI: 10.1074/JBC.M111.231258

(-) Compounds

Molecule 1 - AP4-24H11 ANTIBODY HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - AP4-24H11 ANTIBODY LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2P6G3Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN H:16 , THR H:57 , TYR H:59 , PHE H:67 , SER H:68BINDING SITE FOR RESIDUE P6G H 229
2AC2SOFTWAREASP H:1 , VAL H:2 , SER H:15 , TYR H:27 , ASN H:32 , TYR H:33 , ARG H:66 , ARG H:94BINDING SITE FOR RESIDUE P6G H 230
3AC3SOFTWAREGLU H:95 , GLY H:96 , ASP H:101 , PHE L:36 , THR L:91BINDING SITE FOR RESIDUE P6G H 231

(-) 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  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe H:148 -Pro H:149
2Glu H:150 -Pro H:151
3Trp H:199 -Pro H:200
4Thr L:7 -Pro L:8
5Val L:94 -Pro L:95
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QG7)

(-) Exons   (0, 0)

(no "Exon" information available for 3QG7)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qg7 H   1 DVQLQESGPGLVKPSQSLSLTCTVTGYSITSNYAWNWIRQFPGNKLEWMGFISSYGTTTYNPSLKSRFSITRDTSKNQFFLQLHSVTIEDTGTYFCTREGDYWGQGTTLTVSSAKTTAPSVYPLAPVGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPS 228
                                    10        20        30     |  39        49        59        69        79   |||  86        96|      110       120      |137       147      |162      |173      |185       195|| ||  208       218    ||  
                                                             35A                                             82A||            96|                       127|                154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|            101                        135                 156||     171       183           198 ||  208             226  
                                                                                                               82C                                                            157|                               200|                       
                                                                                                                                                                               162                                202                       


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d3qg7l1 L:1-107 automated matches                                                                               d3qg7l2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qg7 L   1 DVVLTQTPLSLPVSLGDQASISCRSSQRLVHSNGNIYLHWFLQKPGQSPKLLIYKLSSRFSGVPDRFSGSGSGTDFTLKISRVESEDLGIYYCSQTTHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 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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  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  (0, 0)

(no "CATH Domain" information available for 3QG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QG7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3QG7)

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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
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    Thr L:7 - Pro L:8   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
    Val L:94 - Pro L:95   [ RasMol ]  
 

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  3qg7
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 Related Entries

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(-) Related Entries Specified in the PDB File

3qg6