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(-) Description

Title :  S25-2- KDO MONOSACCHARIDE COMPLEX
 
Authors :  H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S.
Date :  26 Jul 11  (Deposition) - 03 Aug 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antigen-Binding Fragment, Fab, Anti-Carbohydrate, Anti-Lps, Antibody, Immunoglobulin, Kdo, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Germline Antibody Recognition Of Distinct Carbohydrate Epitopes.
Nat. Struct. Biol. V. 10 1019 2003
PubMed-ID: 14625588  |  Reference-DOI: 10.1038/NSB1014

(-) Compounds

Molecule 1 - S25-2 FAB (IGG1K) LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - S25-2 FAB (IGG1K) HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:137 , HOH A:341 , HOH A:358 , HIS B:162 , HOH B:349BINDING SITE FOR RESIDUE MG A 216
2AC2SOFTWAREASN A:30A , ARG A:30C , TYR A:32 , SER A:91 , TYR A:92 , ARG A:95 , ARG A:187 , HOH A:214 , TYR B:33 , ARG B:52 , GLU B:100A , HOH B:248 , HOH B:258 , HOH B:313 , HOH B:350 , HOH B:447 , HOH B:507BINDING SITE FOR RESIDUE KDO B 303
3AC3SOFTWAREGLU A:184 , HIS A:188 , GLU B:56 , HOH B:242BINDING SITE FOR RESIDUE ZN B 304

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3B:22 -B:92
4B:138 -B:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:139 -Pro A:140
3Phe B:144 -Pro B:145
4Glu B:146 -Pro B:147
5Trp B:186 -Pro B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3T4Y)

(-) 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:219
                                                                                                                                                                                                                                                            
               SCOP domains d3t4ya1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d3t4ya2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3t4y A    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                        30A|||||                                                                                                                                                                                       
                                                         30B||||                                                                                                                                                                                       
                                                          30C|||                                                                                                                                                                                       
                                                           30D||                                                                                                                                                                                       
                                                            30E|                                                                                                                                                                                       
                                                             30F                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d3t4yb1 B:1-111 Immunoglobulin heavy chain variable domain, VH                                                            d3t4yb2 B:112-211 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee...............eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3t4y B    1 EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDHDGYYERFSYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  211
                                    10        20        30        40        50  ||||| 55        65        75       |84        94      100D|      109       119       129       139       149       159       169       179       189       199       209  
                                                                              52A||||                            82A               100A||||                                                                                                               
                                                                               52B|||                                               100B|||                                                                                                               
                                                                                52C||                                                100C||                                                                                                               
                                                                                 52D|                                                 100D|                                                                                                               
                                                                                  52E                                                  100E
   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  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0 ; only for superseded entry 1Q9V: 1,4)

(no "CATH Domain" information available for 3T4Y, only for superseded entry 1Q9V replaced by 3T4Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T4Y)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3T4Y)

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  Cis Peptide Bonds
    Glu B:146 - Pro B:147   [ RasMol ]  
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    Ser A:7 - Pro A:8   [ RasMol ]  
    Trp B:186 - Pro B:187   [ RasMol ]  
    Tyr A:139 - Pro A:140   [ RasMol ]  
 

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  3t4y
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 Related Entries

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

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