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(-) Description

Title :  STRUCTURE OF THE FAB FRAGMENT OF AB-52, AN ANTIBODY THAT BINDS THE O-ANTIGEN OF FRANCISELLA TULARENSIS
 
Authors :  M. J. Rynkiewicz, Z. Lu, J. H. Hui, J. Sharon, B. A. Seaton
Date :  08 Nov 11  (Deposition) - 25 Jul 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Keywords :  Immunoglobulin, Immune System, O-Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Rynkiewicz, Z. Lu, J. H. Hui, J. Sharon, B. A. Seaton
Structural Analysis Of A Protective Epitope Of The Francisella Tularensis O-Polysaccharide.
Biochemistry V. 51 5684 2012
PubMed-ID: 22747335  |  Reference-DOI: 10.1021/BI201711M

(-) Compounds

Molecule 1 - AB-52 HEAVY CHAIN
    Cell: HYBRIDOMA
    Chains: H, I
    Fragment: FAB FRAGMENT
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - AB-52 LIGHT CHAIN
    Cell: HYBRIDOMA
    Chains: L, M
    Fragment: FAB FRAGMENT
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HILM
Biological Unit 1 (1x): H L 
Biological Unit 2 (1x):  I M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP H:33 , HIS H:35 , GLU H:50 , PHE H:96 , HOH H:432 , HOH H:470 , HOH H:562 , PHE L:96BINDING SITE FOR RESIDUE TRS H 301
2AC2SOFTWAREGLN H:39 , GLY H:44 , LEU H:45 , HOH H:486 , ASP L:85 , PHE L:87 , GLY L:99 , SER L:100BINDING SITE FOR RESIDUE GOL H 302
3AC3SOFTWAREASN L:31 , PHE L:50 , ALA L:51 , SER L:52 , GLY L:66 , HOH L:526BINDING SITE FOR RESIDUE TRS L 301
4AC4SOFTWAREGLN L:37 , LYS L:39 , LYS L:45 , PRO L:59 , PHE L:62 , HOH L:425BINDING SITE FOR RESIDUE GOL L 302
5AC5SOFTWARETRP I:33 , GLU I:50 , HOH I:425 , HOH I:529 , PHE M:96BINDING SITE FOR RESIDUE TRS I 301
6AC6SOFTWAREPRO I:189 , LYS I:209 , GLU I:211 , HOH I:427 , GLN M:156 , VAL M:159BINDING SITE FOR RESIDUE GOL M 301
7AC7SOFTWAREGLN M:37 , LYS M:39 , LYS M:45 , LEU M:47 , PRO M:59 , ARG M:61 , PHE M:62 , GLU M:81 , ASP M:82BINDING SITE FOR RESIDUE GOL M 302

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Ser L:7 -Pro L:8
5Thr L:94 -Pro L:95
6Tyr L:140 -Pro L:141
7Phe I:146 -Pro I:147
8Glu I:148 -Pro I:149
9Trp I:188 -Pro I:189
10Ser M:7 -Pro M:8
11Thr M:94 -Pro M:95
12Tyr M:140 -Pro M:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UJT)

(-) 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 H from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujt H   1 QVQLQQPGSVLVRPGASVKLSCKASGYTFTSSWMHWAKQRPGQGLEWIGEIHPNSGNTNYNEKFKGKATLTVDTSSSTAYVDLSSLTSEDSAVYYCVRGFAYWGQGTLVTVSAAKTTAPSVYPLAPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69   |||  76        86        96 ||    110       120      |136       146       156       166       176       186       196       206       
                                                                              52A                  72A||                        98|                     127|                                                                               
                                                                                                    72B|                        103                      134                                                                               
                                                                                                     72C                                                                                                                                   


Chain I from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujt I   1 QVQLQQPGSVLVRPGASVKLSCKASGYTFTSSWMHWAKQRPGQGLEWIGEIHPNSGNTNYNEKFKGKATLTVDTSSSTAYVDLSSLTSEDSAVYYCVRGFAYWGQGTLVTVSAAKTTAPSVYPLAPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 213
                                    10        20        30        40        50  |     59        69   |||  76        86        96 ||    110       120      |136       146       156       166       176       186       196       206       
                                                                              52A                  72A||                        98|                     127|                                                                               
                                                                                                    72B|                        103                      134                                                                               
                                                                                                     72C                                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d3ujtl1 L:1-107 automated matches                                                                                d3ujtl2 L:108-211 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujt L   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLNSSNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30||||||  34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                        30A|||||                                                                                                                                                                                     
                                                         30B||||                                                                                                                                                                                     
                                                          30C|||                                                                                                                                                                                     
                                                           30D||                                                                                                                                                                                     
                                                            30E|                                                                                                                                                                                     
                                                             30F                                                                                                                                                                                     


Chain M from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d3ujtm1 M:1-107 automated matches                                                                                d3ujtm2 M:108-211 automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ujt M   1 DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLNSSNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPFTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30||||||  34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       
                                                        30A|||||                                                                                                                                                                                     
                                                         30B||||                                                                                                                                                                                     
                                                          30C|||                                                                                                                                                                                     
                                                           30D||                                                                                                                                                                                     
                                                            30E|                                                                                                                                                                                     
                                                             30F
   Legend:   → Mismatch (orange background)
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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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UJT)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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