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(-) Description

Title :  CRYSTAL STRUCTURE OF S25-39 IN COMPLEX WITH KDO
 
Authors :  R. J. Blackler, S. V. Evans
Date :  24 Aug 10  (Deposition) - 06 Apr 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Antibody, Fab, Igg, Carbohydrate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Blackler, C. L. Brooks, D. W. Evans, L. Brade, P. Kosma, H. Brade, S. V. Evans
A Common Nh53K Mutation In The Combining Site Of Antibodies Raised Against Chlamydial Lps Glycoconjugates Significantly Increases Avidity.
Biochemistry V. 50 3357 2011
PubMed-ID: 21405106  |  Reference-DOI: 10.1021/BI101886V

(-) Compounds

Molecule 1 - S25-39 FAB (IGG1K) LIGHT CHAIN
    Chains: A
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C
 
Molecule 2 - S25-39 FAB (IGG1K) HEAVY CHAIN
    Chains: B
    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  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:38 , LYS A:39 , GLY A:41 , GLN A:42BINDING SITE FOR RESIDUE PEG A 223
2AC2SOFTWAREASP B:31 , ASN B:52A , ASP B:97 , HOH B:280 , HOH B:355 , HOH B:417BINDING SITE FOR RESIDUE PEG B 215
3AC3SOFTWAREASN A:27D , TYR A:32 , SER A:91 , TYR A:92 , ARG A:96 , ARG A:188 , TYR B:33 , ARG B:52 , GLU B:100A , HOH B:240 , HOH B:297 , HOH B:325 , HOH B:327 , HOH B:384 , HOH B:458BINDING SITE FOR RESIDUE KDO B 214
4AC4SOFTWAREGLU A:185 , HIS A:189 , GLU B:58 , HOH B:218BINDING SITE FOR RESIDUE ZN B 216

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:195

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:140 -Pro A:141
3Phe B:146 -Pro B:147
4Glu B:148 -Pro B:149
5Trp B:188 -Pro B:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OKD)

(-) 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 d3okda1 A:1-107 automated matches                                                                               d3okda2 A:108-214 automated matches                                                                         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..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3okd A    1 DIVMTQSPSSLAVSAGEKVTMNCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFALTISSVQAEDLAVYYCKQSYNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERANGVLNSWTDQDSKDSTYSMTSTLTLTKDEYERHNSYTCEASHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|||     34        44        54        64        74        84        94|      105       115       125       135       145       155       165       175       185       195       205         
                                                     27A|||||                                                                 94|                                                                                                                      
                                                      27B||||                                                                  96                                                                                                                      
                                                       27C|||                                                                                                                                                                                          
                                                        27D||                                                                                                                                                                                          
                                                         27E|                                                                                                                                                                                          
                                                          27F                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee........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
                3okd B    1 EVKLVESGGGLVQPGGSLRLACATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQSSLYLQMNTLRAEDSATYYCARDHDGYYERFAYWGQGTLVTVSAAATTPPSVYPLAPGSTNSMVTLGCLVKGYFPEPVTVTWNSGSLSTGVHTFPAVLSSDLYTLTSSVTVPSKTWPSETVTCNVAHPASSTKVDKKIVP  212
                                    10        20        30        40        50  |||   57        67        77     |||84        94      |101       111       121      |134       144       154       164       174       184       194       204        
                                                                              52A||                            82A||               100A||                         128|                                                                                
                                                                               52B|                             82B|                100B|                          132                                                                                
                                                                                52C                              82C                 100C
   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 3OKD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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    Tyr A:140 - Pro A:141   [ RasMol ]  
 

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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

3mhl 3mhm 3mhn 3mho 3oke 3okk