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(-) Description

Title :  UNLIGANDED FAB STRUCTURE OF LIPID A-SPECIFIC ANTIBODY S1-15
 
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 :  2.29
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
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 KAPPA) LIGHT CHAIN
    Chains: L, B
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - S1-15 FAB (IGG2B) HEAVY CHAIN
    Chains: H, A
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG H:52 , ARG H:96 , HOH H:403 , HOH H:420 , HOH H:428 , HOH H:447 , HOH H:477BINDING SITE FOR RESIDUE SO4 H 301
2AC2SOFTWAREALA A:33 , ARG A:52 , ARG A:96 , HOH A:407 , HOH A:425BINDING SITE FOR RESIDUE SO4 A 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:195
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:140 -H:195
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Leu L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:146 -Pro H:147
4Gln H:171 -Ser H:172
5Trp H:188 -Pro H:189
6Leu B:94 -Pro B:95
7Tyr B:140 -Pro B:141
8Phe A:146 -Pro A:147
9Glu A:148 -Ser A:149
10Trp A:188 -Pro A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODU)

(-) Sequences/Alignments

Asymmetric 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odu A    1 EVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRHRGAPLYYGNGAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGGSSVTSGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKL  210
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||||   106       116       126||     141       151       161       171       181       191       201         
                                                                              52A||                            82A||               100A|||||||                        127|                                                                             
                                                                               52B|                             82B|                100B||||||                         133                                                                             
                                                                                52C                              82C                 100C|||||                                                                                                         
                                                                                                                                      100D||||                                                                                                         
                                                                                                                                       100E|||                                                                                                         
                                                                                                                                        100F||                                                                                                         
                                                                                                                                         100G|                                                                                                         
                                                                                                                                          100H                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odu B    1 DIQMTQSTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKVLIYYTSRLRSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               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.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odu H    1 EVQLVESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRSKSNNYATYYADSVKDRFTISRDDSQSMLYLQMNNLKTEDTAMYYCVRHRGAPLYYGNGAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGDTTGSSVTSGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEP  212
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||||   106       116       126||     138       148       158       168       178       188       198       208    
                                                                              52A||                            82A||               100A|||||||                        127|                                                                                  
                                                                               52B|                             82B|                100B||||||                         130                                                                                  
                                                                                52C                              82C                 100C|||||                                                                                                              
                                                                                                                                      100D||||                                                                                                              
                                                                                                                                       100E|||                                                                                                              
                                                                                                                                        100F||                                                                                                              
                                                                                                                                         100G|                                                                                                              
                                                                                                                                          100H                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeee....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odu L    1 DIQMTQSTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKVLIYYTSRLRSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4ODU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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4ods 4odt 4odv 4odw 4ody 4odz 4oe0