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(-) Description

Title :  FAB STRUCTURE OF LIPID A-SPECIFIC ANTIBODY S1-15 IN COMPLEX WITH LIPID A CARBOHYDRATE BACKBONE
 
Authors :  O. Haji-Ghassemi, S. V. Evans
Date :  10 Jan 14  (Deposition) - 24 Jun 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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 - S1-15 FAB (IGG2B) HEAVY CHAIN
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - S1-15 FAB (IGG2B KAPPA) LIGHT 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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GP11Ligand/IonGLUCOSAMINE 1-PHOSPHATE
2PG04Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
3Z9M1Ligand/Ion2-AMINO-2-DEOXY-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:32 , GLY H:97 , ALA H:98 , TYR H:100B , Z9M H:302 , HOH H:478 , HOH H:500 , HOH H:513 , HOH H:524BINDING SITE FOR RESIDUE GP1 H 301
2AC2SOFTWARETHR H:31 , TYR H:32 , ALA H:33 , ARG H:52 , ARG H:96 , GLY H:97 , ALA H:98 , GP1 H:301 , HOH H:407 , HOH H:420 , HOH H:491 , HOH H:507BINDING SITE FOR RESIDUE Z9M H 302
3AC3SOFTWAREGLN H:39 , LYS H:43 , GLN L:38 , GLY L:100BINDING SITE FOR RESIDUE PG0 H 303
4AC4SOFTWARELEU H:45 , GLU H:46 , PHE L:98BINDING SITE FOR RESIDUE PG0 L 301
5AC5SOFTWARESER L:63BINDING SITE FOR RESIDUE PG0 L 302
6AC6SOFTWAREHOH L:507 , HOH L:516BINDING SITE FOR RESIDUE PG0 L 303

(-) 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 4ODT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODT)

(-) 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: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........eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odt 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
                4odt 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
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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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 Specified in the PDB File

4ods 4odu 4odv 4odw 4ody 4odz 4oe0