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(-) Description

Title :  CRYSTAL STRUCTURE OF S25-2 IN COMPLEX WITH A 5,6-DEHYDRO-KDO DISACCHARIDE
 
Authors :  C. L. Brooks, S. V. Evans
Date :  08 Oct 12  (Deposition) - 09 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibody, Lps, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Brooks, K. Wimmer, P. Kosma, S. Muller-Loennies, L. Brade, H. Brade, S. V. Evans
Exploring The Cross-Reactivity Of S25-2: Complex With A 5, 6-Dehydro-Kdo Disaccharide.
Acta Crystallogr. , Sect. F V. 69 2 2013
PubMed-ID: 23295476  |  Reference-DOI: 10.1107/S1744309112047422

(-) Compounds

Molecule 1 - ANTIBODY FAB FRAGMENT, LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYDRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTIBODY FAB FRAGMENT, HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    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  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2KTU1Ligand/IonPROP-2-EN-1-YL 3,5-DIDEOXY-ALPHA-D-THREO-OCT-5-EN-2-ULOPYRANOSIDONIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:184 , HIS A:188 , HOH A:408 , GLU B:58BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASN A:137 , HOH A:524 , HIS B:163 , HOH B:599 , HOH B:672BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWARETHR A:181 , TYR B:33 , ASN B:53 , KDO B:302 , HOH B:458 , HOH B:510 , HOH B:572BINDING SITE FOR RESIDUE KTU B 301
4AC4SOFTWARETYR A:32 , SER A:91 , TYR A:92 , ARG A:95 , HOH A:423 , TYR B:33 , ARG B:52 , HIS B:96 , GLU B:100A , KTU B:301 , HOH B:409 , HOH B:418 , HOH B:517 , HOH B:531BINDING SITE FOR RESIDUE KDO B 302

(-) 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 4HGW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HGW)

(-) Exons   (0, 0)

(no "Exon" information available for 4HGW)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains d4hgwa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d4hgwa2 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..hhhhhh..eeeeeeeeeee.....eeeeee..ee..eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hgw A    1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTITSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154|      166       176       186       196       206       
                                                     27A|||||                                                                                                                            154|                                                        
                                                      27B||||                                                                                                                             157                                                        
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4hgwb1 B:1-112 Immunoglobulin heavy chain variable domain, VH                                                           d4hgwb2 B:113-211 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.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hgw B    1 EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDHDGYYERFSWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP  211
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |101       111       121   ||  138       148       158       168       178       188       198       208   
                                                                              52A||                            82A||               100A||                      125|                                                                              
                                                                               52B|                             82B|                100B|                       133                                                                              
                                                                                52C                              82C                 100C
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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)

(no "CATH Domain" information available for 4HGW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HGW)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4HGW)

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  Cis Peptide Bonds
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