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(-) Description

Title :  UNLIGANDED FAB STRUCTURE OF LIPID A-SPECIFIC ANTIBODY A6
 
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 :  2.72
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 - A6 FAB (IGG2B KAPPA) LIGHT CHAIN
    Chains: L, B
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - A6 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:39 , THR A:40 , PRO A:41 , LYS A:43BINDING SITE FOR RESIDUE TRS A 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:139 -A:194
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:139 -H:194
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (20, 20)

Asymmetric Unit
No.Residues
1Leu L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Asp H:61 -Thr H:62
4Gly H:127 -Cys H:128
5Phe H:145 -Pro H:146
6Glu H:147 -Ser H:148
7Ser H:155 -Gly H:156
8Ser H:185 -Thr H:186
9Trp H:187 -Pro H:188
10Leu B:94 -Pro B:95
11Asn B:137 -Asn B:138
12Tyr B:140 -Pro B:141
13Glu A:42 -Lys A:43
14Asn A:98 -Tyr A:99
15Tyr A:99 -Val A:100
16Gly A:132 -Ser A:133
17Phe A:145 -Pro A:146
18Glu A:147 -Ser A:148
19Ser A:160 -Ser A:161
20Trp A:187 -Pro A:188

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ODW)

(-) 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:208
                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......ee.......eeeeeeehhh.eeeeeee..hhhhheeeeeeeee.......eeeee...eeeee........eeeee....eeeeeeeeeee.....eeeee...eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odw A    2 VKLVESGGGLVKLGGSLKLSCAASGFTFSSYYMSWVRQTPEKRLELVAAINSNGGNTYYPDTVKGLFTISRDNAKNTLYLQMSRLKSEDTALYYCTRLYGNYVRIHTMDYWGQGTSVTVSSAKTTPPSVYPLAPGSSVTLGCLVKGYFPESVTVTWNSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKL  209
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||102       112       122   ||  137       147       161       171       181       191       201        
                                                                             52A                            82A||               100A||||                       126|                    155|                                                 
                                                                                                             82B|                100B|||                        132                     160                                                 
                                                                                                              82C                 100C||                                                                                                    
                                                                                                                                   100D|                                                                                                    
                                                                                                                                    100E                                                                                                    


Chain B 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.....eeeeeehhhee.......eeeeee..eeeeee.........eeeeee.......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odw B    1 DIVLTQSTSSLSASLGDRVTITCRASQDIRNYLSWYQQRPDGTVKLLIYYTSKLHSGVPSRFSGSGSGTDYSLTITNLEQEDIATYFCQQGKTLPLYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209    
                                                                                                                         95A                                                                                                                      


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeeeee...eeeee........eeeee.....eeeeeeeeee.....eeee........eeeeeeeee..eeeeeeeeee..........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odw H    2 VKLVESGGGLVKLGGSLKLSCAASGFTFSSYYMSWVRQTPEKRLELVAAINSNGGNTYYPDTVKGLFTISRDNAKNTLYLQMSRLKSEDTALYYCTRLYGNYVRIHTMDYWGQGTSVTVSSAKTTPPSVYPLAPGCSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEP  211
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||102       112       122     ||137       147       157       167       177       187       197       207    
                                                                             52A                            82A||               100A||||                         128|                                                                             
                                                                                                             82B|                100B|||                          134                                                                             
                                                                                                              82C                 100C||                                                                                                          
                                                                                                                                   100D|                                                                                                          
                                                                                                                                    100E                                                                                                          


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.....eeeeeehhhee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4odw L    1 DIVLTQSTSSLSASLGDRVTITCRASQDIRNYLSWYQQRPDGTVKLLIYYTSKLHSGVPSRFSGSGSGTDYSLTITNLEQEDIATYFCQQGKTLPLYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209    
                                                                                                                         95A
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4ODW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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4ods 4odt 4odu 4odv 4ody 4odz 4oe0