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(-) Description

Title :  S25-2- A(2-4)KDO DISACCHARIDE COMPLEX
 
Authors :  H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S.
Date :  29 Jul 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
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 Common: MOUSE
    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 Common: MOUSE
    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  (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 , HOH A:431 , HIS B:162BINDING SITE FOR RESIDUE MG A 216
2AC2SOFTWAREASP A:1 , HOH A:370BINDING SITE FOR RESIDUE MG A 217
3AC3SOFTWAREGLU A:184 , HIS A:188 , HOH A:316 , GLU B:56BINDING SITE FOR RESIDUE ZN A 218
4AC4SOFTWAREARG A:30C , ARG A:154 , ASN A:156 , TYR B:33 , ASN B:52D , KDO B:303BINDING SITE FOR RESIDUE KDA B 302
5AC5SOFTWARETYR 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:267 , HOH B:268 , HOH B:279 , HOH B:280 , KDA B:302BINDING 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: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 3T77)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T77)

(-) Exons   (0, 0)

(no "Exon" information available for 3T77)

(-) 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
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
        Q52L64_MOUSE     21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYPLTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  240
               SCOP domains d3t77a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d3t77a2 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.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...-..ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3t77 A    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYN-LRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20        30||||||  34        44        54        64        74        84        |-|      103       113       123       133       143       153       163       173       183       193       203       213
                                                        30A|||||                                                             93 |                                                                                                                       
                                                         30B||||                                                               94                                                                                                                       
                                                          30C|||                                                                                                                                                                                        
                                                           30D||                                                                                                                                                                                        
                                                            30E|                                                                                                                                                                                        
                                                             30F                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d3t77b1 B:1-111 Immunoglobulin heavy chain variable domain, VH                                                            d3t77b2 B:112-213 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..........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3t77 B    1 EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDHDGYYERFSYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC  213
                                    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 1Q9T: 1,4)

(no "CATH Domain" information available for 3T77, only for superseded entry 1Q9T replaced by 3T77)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T77)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q52L64_MOUSE | Q52L64)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3t77
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 Related Entries

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

UniProtKB/TrEMBL
        Q52L64_MOUSE | Q52L64: 1a3r 1bbd 1h3p 1jgu 1jgv 1q9w 2fd6 2r1w 2r1x 2r1y 2r23 2r2b 2r2h

(-) Related Entries Specified in the PDB File

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