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(-) Description

Title :  HIGH RESOLUTION STRUCTURES OF ANTIBODY FAB FRAGMENT COMPLEXED WITH CELL-SURFACE OLIGOSACCHARIDE OF PATHOGENIC SALMONELLA
 
Authors :  A. Zdanov, M. Cygler
Date :  25 Oct 93  (Deposition) - 31 Jan 94  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Cygler, S. Wu, A. Zdanov, D. R. Bundle, D. R. Rose
Recognition Of A Carbohydrate Antigenic Determinant Of Salmonella By An Antibody.
Biochem. Soc. Trans. V. 21 437 1993
PubMed-ID: 7689495
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ABE1Ligand/IonABEQUOSE
2GLA1Ligand/IonALPHA D-GALACTOSE
3MAN1Ligand/IonALPHA-D-MANNOSE
4RAM1Ligand/IonALPHA-L-RHAMNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMAN H:522 , RAM H:524 , HOH H:603 , HOH H:768 , TRP L:93BINDING SITE FOR RESIDUE GLA H 521
2AC2SOFTWAREHIS H:351 , GLA H:521 , ABE H:523 , RAM H:524 , HOH H:602BINDING SITE FOR RESIDUE MAN H 522
3AC3SOFTWARETRP H:283 , HIS H:285 , GLY H:350 , HIS H:351 , GLY H:352 , MAN H:522 , HOH H:601 , HOH H:603 , TRP L:98BINDING SITE FOR RESIDUE ABE H 523
4AC4SOFTWARETRP H:283 , ASN H:305 , ALA H:307 , GLA H:521 , MAN H:522BINDING SITE FOR RESIDUE RAM H 524

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:272 -H:346
2H:395 -H:450
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:401 -Pro H:402
3Glu H:403 -Pro H:404
4Trp H:443 -Pro H:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MFC)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains d1mfch1 H:251-367 Immunoglobulin heavy chain variable domain, VH                                                     d1mfch2 H:368-468 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 1mfcH01 H:251-368 Immunoglobulins                                                                                     1mfcH02 H:369-467 Immunoglobulins                                                            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eeeeeeeeeeee..eeeeeeeeeeee.hhhhheeeeeeeeeeeeeeeeeeee....eeeee.....eeeeeee...eeeeeeeee.....eeeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..eeeeeee.....eeeeeeeeeee.eeeeeeeeeee...hhhhh---------------------- Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeeeeee Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mfc H 251 EVQVQQSGTVLARPGASVKMSCKASGYTFTNYWMHWIKQRPGQGLEWIGAIYPGNSATFYNHKFRAKTKLTAVTSTITAYMELSSLTNEDSAVYYCTRGGHGYYGDYWGQGASLTVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 468
                                   260       270       280       290       300       310       320       330       340       350       360       370       380  ||   396       406       416       426       436       446       456       466  
                                                                                                                                                              383|                                                                              
                                                                                                                                                               390                                                                              


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1mfcl1 L:1-111 Immunoglobulin light chain lambda variable domain, VL-lambda                                   d1mfcl2 L:112-212 Immunoglobulin light chain lambda constant domain, CL-lambda                        SCOP domains
               CATH domains 1mfcL01 L:1-110 Immunoglobulins                                                                               1mfcL02 L:111-212 Immunoglobulins                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) eeeeeeeeeeee...--------hhhh..hhhhh.eeeeeee.eeeeeeee...eeee......eeeeeeeeeeeeeeee....eeeeeeeee...eeeeeeeeeeeee....----------hhhhhhhh.eeeeeeeeeee..eeeeeeeeee.....eeeeeeeeee.eeeeeeeeeeeehhhhhhh.eeeeeeeeeeeeeeeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) ---------------eeeeeeeeeee---------------------------------------------------------------------------------------eeeeeeeeeee---------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mfc L   1 QAVVTQESALTTSPGETVTLTCRSSTGTVTSGNHANWVQEKPDHLFTGLIGDTNNRAPGVPARFSGSLIGDKAALTITGAQPEDEAIYFCALWCNNHWIFGGGTKLTVLGQPKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSRA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (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 1MFC)

(-) Gene Ontology  (0, 0)

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

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