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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAINST VIBRIO CHOLERAE O1 IN COMPLEX WITH ANTIGEN
 
Authors :  P. M. Alzari, H. Souchon
Date :  10 Jun 00  (Deposition) - 02 Aug 00  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Anti-Carbohydrate Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Villeneuve, H. Souchon, M. M. Riottot, J. C. Mazie, P. Lei, C. P. Glaudemans, P. Kovac, J. M. Fournier, P. M. Alzari
Crystal Structure Of An Anti-Carbohydrate Antibody Directed Against Vibrio Cholerae O1 In Complex With Antigen: Molecular Basis For Serotype Specificity.
Proc. Natl. Acad. Sci. Usa V. 97 8433 2000
PubMed-ID: 10880560  |  Reference-DOI: 10.1073/PNAS.060022997

(-) Compounds

Molecule 1 - ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Secretion: ASCITES
 
Molecule 2 - ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Secretion: ASCITES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MGS1Ligand/Ion1,2-O-DIMETHYL-4-[2,4-DIHYDROXY-BUTYRAMIDO]-4,6-DIDEOXY-ALPHA-D-MANNOPYRANOSIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:31 , TYR H:32 , ASP H:33 , HIS H:99 , TYR H:101 , ALA H:102 , TRP L:98BINDING SITE FOR RESIDUE MGS H 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:144 -H:199
3L:22 -L:90
4L:137 -L:196

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr L:143 -Pro L:144
2Phe H:150 -Pro H:151
3Glu H:152 -Pro H:153
4Trp H:192 -Pro H:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F4X)

(-) Exons   (0, 0)

(no "Exon" information available for 1F4X)

(-) Sequences/Alignments

Asymmetric/Biological 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:216
                                                                                                                                                                                                                                                        
               SCOP domains d1f4xh1 H:1-117 Immunoglobulin heavy chain variable domain, VH                                                       d1f4xh2 H:118-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1f4xH01 H:1-117 Immunoglobulins                                                                                      1f4xH02 H:118-216 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhh.ee........eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f4x H   1 EVQLEESGGGLVTPGGSLRLSCAASGYVFSTYDMSWVRQTPEKRLEWVAFISSGGGRTSYPDTVKGRFTISRDDAKNTLYLQMSSLQSEDTAMYYCTRHFYAVLDYWGRGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains d1f4xl1 L:1-110 Immunoglobulin light chain lambda variable domain, VL-lambda                                  d1f4xl2 L:111-210 Immunoglobulin light chain lambda constant domain, CL-lambda                       SCOP domains
               CATH domains 1f4xL01 L:1-110 Immunoglobulins                                                                               1f4xL02 L:111-209 Immunoglobulins                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eeee....eeeeeeee.....hhhhh.eeeeee...eeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee........eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeeehhhhhhh..eeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f4x L   1 QAVVTQESALTTSPGETVTLTCRSSTGTVTTSNYANWVQEKPDHLFTGLIGATNNRAAGVPVRFSGSLIGGKAALTITGAQTEDEAIYFCALWYSGHWVFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTNPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLS 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F4X)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1F4X)

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  Cis Peptide Bonds
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  1f4x
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1f4w 1F4W CONTAINS THE UNLIGANDED FAB FRAGMENT
1f4y