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(-) Description

Title :  CRYSTAL STRUCTURE OF S54-10 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.4)KDO(2.4)KDO
 
Authors :  C. L. Brooks, S. Muller-Loennies, S. N. Borisova, L. Brade, P. Kosma, T. Hirama, C. R. Mackenzie, H. Brade, S. V. Evans
Date :  24 Jun 09  (Deposition) - 12 Jan 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Antibody, Fab, Igg, Carbohydrate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Brooks, S. Muller-Loennies, S. N. Borisova, L. Brade, P. Kosma, T. Hirama, C. R. Mackenzie, H. Brade, S. V. Evans
Antibodies Raised Against Chlamydial Lipopolysaccharide Antigens Reveal Convergence In Germline Gene Usage And Differential Epitope Recognition
Biochemistry V. 49 570 2010
PubMed-ID: 20000757  |  Reference-DOI: 10.1021/BI9011308

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN
    Chains: A, C
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: S54-10 FAB LIGHT CHAIN
    Other Details - Source: ASCITES
    Strain: BALB/C
 
Molecule 2 - IMMUNOGLUBULIN HEAVY CHAIN
    Chains: B, D
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: S54-10 FAB HEAVY CHAIN
    Other Details - Source: 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1KDA2Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO4Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1KDA1Ligand/Ion(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
2KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:27D , ARG A:27F , KDO A:215 , KDO A:216 , PHE B:99BINDING SITE FOR RESIDUE KDA A 214
2AC2SOFTWAREKDA A:214 , KDO A:216 , HOH A:263 , TYR B:33 , LYS B:53 , PHE B:99BINDING SITE FOR RESIDUE KDO A 215
3AC3SOFTWARESER A:91 , TYR A:92 , ARG A:95 , KDA A:214 , KDO A:215 , HOH A:236 , TYR B:33 , ARG B:52 , ASP B:100CBINDING SITE FOR RESIDUE KDO A 216
4AC4SOFTWAREASN C:27D , ARG C:27F , PHE D:99 , KDO D:215 , KDO D:216BINDING SITE FOR RESIDUE KDA D 214
5AC5SOFTWARETYR D:33 , LYS D:53 , PHE D:99 , KDA D:214 , KDO D:216BINDING SITE FOR RESIDUE KDO D 215
6AC6SOFTWARESER C:91 , TYR C:92 , ARG C:95 , TYR D:33 , ARG D:52 , MET D:96 , ASP D:100C , KDA D:214 , KDO D:215 , HOH D:267BINDING SITE FOR RESIDUE KDO D 216

(-) 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  (15, 15)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:139 -Pro A:140
3Gly B:100B-Asp B:100C
4Gly B:144 -Tyr B:145
5Phe B:146 -Pro B:147
6Glu B:148 -Pro B:149
7Trp B:188 -Pro B:189
8Ser C:7 -Pro C:8
9Tyr C:139 -Pro C:140
10Ser C:202 -Pro C:203
11Gly D:100B-Asp D:100C
12Gly D:144 -Tyr D:145
13Phe D:146 -Pro D:147
14Glu D:148 -Pro D:149
15Trp D:188 -Pro D:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I02)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I02)

(-) Exons   (0, 0)

(no "Exon" information available for 3I02)

(-) 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 d3i02a1 A:1-106 automated matches                                                                               d3i02a2 A:107-213 automated matches                                                                         SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3i02A02 A:108-213 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3i02 A    1 DIVMTQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIFWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLRTFGRGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                     27A|||||                                                                                                                                                                                          
                                                      27B||||                                                                                                                                                                                          
                                                       27C|||                                                                                                                                                                                          
                                                        27D||                                                                                                                                                                                          
                                                         27E|                                                                                                                                                                                          
                                                          27F                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i02B01 B:1-113 Immunoglobulins                                                                                             3i02B02 B:114-212 Immunoglobulins                                                              - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee...hhhhh.........eeeee........eeeee.......eeeeeeee.......eeee.hhh....eee...ee....eeeeeeeee..........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3i02 B    1 EVMLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKVKGYTIDYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDMRRFDDGDAMDYWGQGTLVTVSAAKTTPPSVYPLAPGTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|      109       119       133       143       153       163       173       183       193       203       213
                                                                              52A||                            82A||               100A||||                        127|                                                                                 
                                                                               52B|                             82B|                100B|||                         132                                                                                 
                                                                                52C                              82C                 100C||                                                                                                             
                                                                                                                                      100D|                                                                                                             
                                                                                                                                       100E                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                     
               SCOP domains d3i02c1 C:1-106 automated matches                                                                               d3i02c2 C:107-207 automated matches                                                  SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3i02C02 C:108-207 Immunoglobulins                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee......eeeee.........eeeeeeeeee.......eee........eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3i02 C    1 DIVMTQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPKLLIFWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYNLRTFGRGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDIGVLNSWTDQDSKDSTYSMSSTLTLTKDERHNTCEATHKTSTSPIVKS  207
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       157       167       177      |189|      201      
                                                     27A|||||                                                                                                                 143|                        184| ||               
                                                      27B||||                                                                                                                  157                         187 ||               
                                                       27C|||                                                                                                                                                189|               
                                                        27D||                                                                                                                                                 192               
                                                         27E|                                                                                                                                                                   
                                                          27F                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i02D01 D:1-113 Immunoglobulins                                                                                             3i02D02 D:114-212 Immunoglobulins                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeee............ee...eeeee........eeeee....eeeeeee.......eeee.hhh....eee...ee....eeeeeeee...hhhhhh..eeeee.....eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3i02 D    1 EVMLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKVKGYTIDYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDMRRFDDGDAMDYWGQGTLVTVSAAKTTPPSVYPLAPGVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASVDKKIVP  212
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|      109       119       137       147       157       167       177       187       197    || 210  
                                                                              52A||                            82A||               100A||||                        127|                                                               202|      
                                                                               52B|                             82B|                100B|||                         136                                                                206      
                                                                                52C                              82C                 100C||                                                                                                     
                                                                                                                                      100D|                                                                                                     
                                                                                                                                       100E
   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)
1a3i02A02A:108-213
1b3i02C02C:108-207
1c3i02B02B:114-212
1d3i02D02D:114-212
1e3i02B01B:1-113
1f3i02D01D:1-113

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I02)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3I02)

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(-) Related Entries Specified in the PDB File

3hzk CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.4)KDO
3hzm CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO
3hzv CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.8)KDO(2.4)KDO
3hzy CRYSTAL STRUCTURE OF S73-2 ANTIBODY IN COMPLEX WITH ANTIGEN KDO(2.4)KDO(2.4)KDO