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(-) Description

Title :  CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.4)KDO
 
Authors :  C. L. Brooks, S. Muller-Loennies, S. N. Borisova, L. Brade, P. Kosma, T. Hirama, C. R. Mackenzie, H. Brade, S. V. Evans
Date :  23 Jun 09  (Deposition) - 12 Jan 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibody, Fab, Igg, Carbohydrate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Brooks, S. Muller-Loennies, S. N. Borisova, L. Brade, P. Kosma, T. Hirama, C. R. Mackenzie, H. Brade, S. V. Evans
Antibodies Raised Against Chlamydial Lipopolysaccharide Antigens Reveal Convergence In Germline Gene Usage And Differential Epitope Recognition
Biochemistry V. 49 570 2010
PubMed-ID: 20000757  |  Reference-DOI: 10.1021/BI9011308

(-) Compounds

Molecule 1 - S73-2 FAB (IGG1K) LIGHT CHAIN
    Chains: A
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C
 
Molecule 2 - S73-2 FAB (IGG1K) HEAVY CHAIN
    Chains: B
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3MG2Ligand/IonMAGNESIUM ION
4ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:137 , ASP A:166 , HIS B:163BINDING SITE FOR RESIDUE MG A 216
2AC2SOFTWAREHIS A:188 , ARG B:52 , GLU B:58 , ZN B:215BINDING SITE FOR RESIDUE MG A 217
3AC3SOFTWAREHIS A:188 , MG A:217 , HOH A:290 , GLU B:58BINDING SITE FOR RESIDUE ZN B 215
4AC4SOFTWAREGLU A:184 , HOH A:241 , TYR B:33 , LYS B:53 , KDO B:303BINDING SITE FOR RESIDUE KDA B 302
5AC5SOFTWARESER A:91 , TYR A:92 , ARG A:95 , ARG A:187 , TYR B:33 , ARG B:52 , ILE B:96 , ASP B:100E , HOH B:232 , HOH B:251 , HOH B:275 , KDA B:302 , HOH B:305BINDING SITE FOR RESIDUE KDO B 303

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3B:22 -B:92
4B:139 -B:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:139 -Pro A:140
3Phe B:145 -Pro B:146
4Glu B:147 -Pro B:148
5Trp B:187 -Pro B:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HZK)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains d3hzka1 A:1-106 automated matches                                                                               d3hzka2 A:107-212 automated matches                                                                        SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3hzkA02 A:108-210 Immunoglobulins                                                                      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3hzk A    1 DIVMTQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLRTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKSIAVKWKIDGSERQNGVLNSWTDQDKKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  212
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
                                                     27A|||||                                                                                                                                                                                         
                                                      27B||||                                                                                                                                                                                         
                                                       27C|||                                                                                                                                                                                         
                                                        27D||                                                                                                                                                                                         
                                                         27E|                                                                                                                                                                                         
                                                          27F                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3hzkB01 B:1-113 Immunoglobulins                                                                                               3hzkB02 B:114-211 Immunoglobulins                                                              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee..............ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3hzk B    1 EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLAFIRNKAKGYTTEYSSSVKGRFTISRDNSQSFLYLQMNTLRAEDSATYYCARDINPGSDGYYDALDYWGQGTSVTVSRAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  212
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||    107       117       127||     140       150       160       170       180       190       200       210  
                                                                              52A||                            82A||               100A||||||                         128|                                                                                
                                                                               52B|                             82B|                100B|||||                          132                                                                                
                                                                                52C                              82C                 100C||||                                                                                                             
                                                                                                                                      100D|||                                                                                                             
                                                                                                                                       100E||                                                                                                             
                                                                                                                                        100F|                                                                                                             
                                                                                                                                         100G
   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, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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  3hzk
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3hzm CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO
3hzv CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.8)KDO(2.4)KDO
3hzy CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.4)KDO(2.4)KDO
3i02 CRYSTAL STRUCTURE OF HOMOLOGOUS S54-10 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.4)KDO(2.4)KDO