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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  UNLIGANDED FAB STRUCTURE OF LIPID A-SPECIFIC ANTIBODY S55-3
 
Authors :  O. Haji-Ghassemi, S. V. Evans
Date :  10 Jan 14  (Deposition) - 01 Jul 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Carbohydrate Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Haji-Ghassemi, S. Muller-Loennies, T. Rodriguez, L. Brade, P. Kosma, H. Brade, S. V. Evans
Structural Basis For Antibody Recognition Of Lipid A: Insights To Polyspecificity Toward Single-Stranded Dna.
J. Biol. Chem. V. 290 19629 2015
PubMed-ID: 26085093  |  Reference-DOI: 10.1074/JBC.M115.657874

(-) Compounds

Molecule 1 - S55-3 FAB (IGG2B) HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - S55-3 FAB (IGG2B) HEAVY CHAIN
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4ODS)

(-) Sites  (0, 0)

(no "Site" information available for 4ODS)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:128 -L:214
3H:140 -H:195
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Ser H:149
3Trp H:188 -Pro H:189
4Ser L:7 -Pro L:8
5Asn L:76 -Pro L:77
6Asp L:94 -Pro L:95
7Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ODS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODS)

(-) 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 H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....eeeeeee.........eeeeee......eeeeee......eee........eeeee....eeeeee...hhhhheeeeeeee.........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ods H    1 EVQLVESGGDLVKPGGSLKLSCAGSGITFSGYGMSWVRQTPDKSLEWVALISNGGSYAYYSDSVKGRFTISRDNAKNTLYLQMSSLRSDDTAIYYCARHKGLRGGTNAMDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEPS  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111       121       131       141       151     ||164       174       184       194       204         
                                                                              52A                            82A||               100A||||                                                      157|                                                    
                                                                                                              82B|                100B|||                                                       161                                                    
                                                                                                               82C                 100C||                                                                                                              
                                                                                                                                    100D|                                                                                                              
                                                                                                                                     100E                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ods L    1 DIVLTQSPASLAVSLGQRATIFCRASETVDSYGNSFMHWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27A|||                                                                                                                                                                                           
                                                      27B||                                                                                                                                                                                           
                                                       27C|                                                                                                                                                                                           
                                                        27D
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4ODS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Sites
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  Cis Peptide Bonds
    Asn L:76 - Pro L:77   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Glu H:148 - Ser H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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(-) Related Entries Specified in the PDB File

4odt 4odu 4odv 4odw 4ody 4odz 4oe0