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(-) Description

Title :  STRUCTURE OF S67-27 IN COMPLEX WITH KDO(2.8)KDO
 
Authors :  C. L. Brooks, R. J. Blackler, S. V. Evans
Date :  05 Aug 09  (Deposition) - 06 Oct 09  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibody, Kdo, Chlamydia, Lps, Fab, Carbohydrate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Brooks, R. J. Blackler, G. Sixta, P. Kosma, S. Muller-Loennies, L. Brade, T. Hirama, C. R. Mackenzie, H. Brade, S. V. Evans
The Role Of Cdr H3 In Antibody Recognition Of A Synthetic Analog Of A Lipopolysaccharide Antigen.
Glycobiology V. 20 138 2010
PubMed-ID: 19767317  |  Reference-DOI: 10.1093/GLYCOB/CWP150
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLUBILIN LIGHT CHAIN (IGG3)
    Chains: A, C
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C
 
Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN (IGG3)
    Chains: B, D
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: ASCITES
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1KDA2Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO1Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:27F , LYS B:53 , HOH B:219 , KDO B:303BINDING SITE FOR RESIDUE KDA B 302
2AC2SOFTWAREASN A:27D , ARG A:27F , SER A:91 , ASN A:92 , ARG A:95 , TYR B:33 , ARG B:52 , ILE B:96 , GLU B:100E , KDA B:302BINDING SITE FOR RESIDUE KDO B 303
3AC3SOFTWAREARG B:52 , GLU B:58 , GLU D:58 , MG D:214BINDING SITE FOR RESIDUE MG B 214
4AC4SOFTWAREARG C:27F , LYS D:53 , KDO D:303BINDING SITE FOR RESIDUE KDA D 302
5AC5SOFTWAREASN C:27D , SER C:91 , ASN C:92 , ARG C:95 , TYR D:33 , ARG D:52 , ILE D:96 , GLU D:100E , HOH D:226 , KDA D:302BINDING SITE FOR RESIDUE KDO D 303
6AC6SOFTWAREGLU B:58 , MG B:214 , ARG D:52 , GLU D:58BINDING SITE FOR RESIDUE MG D 214

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3B:22 -B:92
4B:140 -B:195
5C:23 -C:88
6C:133 -C:193
7D:22 -D:92
8D:140 -D:195

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:139 -Pro A:140
3Phe B:146 -Pro B:147
4Glu B:148 -Pro B:149
5Trp B:188 -Pro B:189
6Ser C:7 -Pro C:8
7Tyr C:139 -Pro C:140
8Phe D:146 -Pro D:147
9Glu D:148 -Pro D:149
10Trp D:188 -Pro D:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IJY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IJY)

(-) Exons   (0, 0)

(no "Exon" information available for 3IJY)

(-) 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:215
                                                                                                                                                                                                                                                        
               SCOP domains d3ijya1 A:2-106 automated matches                                                                              d3ijya2 A:107-210 automated matches                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------3ijyA02 A:108-210 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ijy A    2 IVMTQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSNNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  210
                                    11        21      |27D||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
                                                    27A|||||                                                                                                                                                                                       
                                                     27B||||                                                                                                                                                                                       
                                                      27C|||                                                                                                                                                                                       
                                                       27D||                                                                                                                                                                                       
                                                        27E|                                                                                                                                                                                       
                                                         27F                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ijyB01 B:1-113 Immunoglobulins                                                                                               3ijyB02 B:114-213 Immunoglobulins                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...................eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ijy B    1 EVMLVESGGGLVQPGNSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDISPSYGVYYEGFAYWGQGTLVTVSAATTTAPSVYPLVPGGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||    107       117       127|      142       152       162       172       182       192       202       212 
                                                                              52A||                            82A||               100A||||||                        127|                                                                                
                                                                               52B|                             82B|                100B|||||                         133                                                                                
                                                                                52C                              82C                 100C||||                                                                                                            
                                                                                                                                      100D|||                                                                                                            
                                                                                                                                       100E||                                                                                                            
                                                                                                                                        100F|                                                                                                            
                                                                                                                                         100G                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d3ijyc1 C:2-106 automated matches                                                                              d3ijyc2 C:107-212 automated matches                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------3ijyC02 C:108-210 Immunoglobulins                                                                      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ijy C    2 IVMTQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSNNLRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNREC  212
                                    11        21      |27D||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                    27A|||||                                                                                                                                                                                         
                                                     27B||||                                                                                                                                                                                         
                                                      27C|||                                                                                                                                                                                         
                                                       27D||                                                                                                                                                                                         
                                                        27E|                                                                                                                                                                                         
                                                         27F                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ijyD01 D:1-113 Immunoglobulins                                                                                               3ijyD02 D:114-213 Immunoglobulins                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeee...................eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ijy D    1 EVMLVESGGGLVQPGNSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDISPSYGVYYEGFAYWGQGTLVTVSAATTTAPSVYPLVPGSSVTLGCLVKGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQTVICNVAHPASKTELIKRIEPR  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||    107       117       127|      143       153       163       173       183       193       203       213
                                                                              52A||                            82A||               100A||||||                        127|                                                                               
                                                                               52B|                             82B|                100B|||||                         134                                                                               
                                                                                52C                              82C                 100C||||                                                                                                           
                                                                                                                                      100D|||                                                                                                           
                                                                                                                                       100E||                                                                                                           
                                                                                                                                        100F|                                                                                                           
                                                                                                                                         100G
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Mouse (Mus musculus) (152)
1a3ijyC02C:108-210
1b3ijyA02A:108-210
1c3ijyB02B:114-213
1d3ijyD02D:114-213
1e3ijyB01B:1-113
1f3ijyD01D:1-113

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IJY)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3IJY)

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  3ijy
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3IJY)

(-) Related Entries Specified in the PDB File

3ijh SAME PROTEIN WITH DIFFERENT LIGAND
3ijs SAME PROTEIN WITH DIFFERENT LIGAND
3ikc