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(-) Description

Title :  FAB STRUCTURE OF ANTIBODY S1-15 IN COMPLEX WITH SSDNA DNA, 5'-P5(DT)P-3'
 
Authors :  O. Haji-Ghassemi, S. V. Evans
Date :  08 Apr 15  (Deposition) - 24 Jun 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,E,H,L
Keywords :  Antibody, Fab, Carbohydrate, Lipid A, Dna, Immune System-Dna Complex (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 - S1-15 FAB (IGG2B) HEAVY CHAIN
    Chains: H
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C
 
Molecule 2 - S1-15 FAB (IGG2B KAPPA) LIGHT CHAIN
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C
 
Molecule 3 - 5'-D(P*TP*TP*TP*TP*T)-3'
    Chains: E, A
    Engineered: YES
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : AEHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1THP1Mod. NucleotideTHYMIDINE-3',5'-DIPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4Z8F)

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z8F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z8F)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z8F)

(-) 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:DNA  Length:3
                                    
                4z8f A    6 TTx    8
                              |
                              |
                              8-THP


Chain E from PDB  Type:DNA  Length:4
                                     
                4z8f E   10 TTTT   13


Chain H from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee..hhhhhh....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.........eeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z8f H    1 EVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRHRGAPLYYGNGAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEP  212
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||||   106       116       126       136       146       156       166       176       186       196       206      
                                                                              52A||                            82A||               100A|||||||                                                                                                                
                                                                               52B|                             82B|                100B||||||                                                                                                                
                                                                                52C                              82C                 100C|||||                                                                                                                
                                                                                                                                      100D||||                                                                                                                
                                                                                                                                       100E|||                                                                                                                
                                                                                                                                        100F||                                                                                                                
                                                                                                                                         100G|                                                                                                                
                                                                                                                                          100H                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z8f L    1 DIQMTQSTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKVLIYYTSRLRSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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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 4Z8F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z8F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z8F)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4Z8F)

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  Cis Peptide Bonds
    Glu H:148 - Ser H:149   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
    Tyr L:140 - Pro L: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

4odt FAB OF SAME ANTIBODY IN COMPLEX WITH LIPID A CARBOHYDRATE BACKBONE
4odu FAB OF SAME ANTIBODY UNLIGANDED.
4z95