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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMANIZED FAB (HU3S193) IN COMPLEX WITH THE LEWIS Y TETRASACCHARIDE
 
Authors :  P. A. Ramsland, W. Farrugia, T. M. Bradford, P. M. Hogarth, A. M. Scott
Date :  13 Jan 04  (Deposition) - 13 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin Fold, Beta Barrel, Humanized Antibody, Antigen Binding Fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Ramsland, W. Farrugia, T. M. Bradford, P. M. Hogarth, A. M. Scott
Structural Convergence Of Antibody Binding Of Carbohydrate Determinants In Lewis Y Tumor Antigens
J. Mol. Biol. V. 340 809 2004
PubMed-ID: 15223322  |  Reference-DOI: 10.1016/J.JMB.2004.05.037

(-) Compounds

Molecule 1 - HU3S193 FAB FRAGMENT, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: NS0 MURINE MYELOMA CELLS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Organism Common: HUMAN, HOUSE MOUSE
    Organism Scientific: HOMO SAPIENS, MUS MUSCULUS
    Organism Taxid: 9606,10090
    Other Details: MURINE COMPLEMENTARITY DETERMINING REGIONS GRAFTED ONTO HUMAN FRAMEWORK AND CONSTANT SEQUENCES
    Strain: ,
 
Molecule 2 - HU3S193 FAB FRAGMENT, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: NS0 MURINE MYELOMA CELLS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Organism Common: HOUSE MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090,9606
    Other Details: MURINE COMPLEMENTARITY DETERMINING REGIONS GRAFTED ONTO HUMAN FRAMEWORK AND CONSTANT SEQUENCES
    Strain: ,

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS H:212 , VAL H:213 , ASP H:214 , GAL H:224 , NDG H:225 , HOH H:265 , HOH H:381 , HIS L:31 , ASN L:33BINDING SITE FOR RESIDUE FUC H 223
2AC2SOFTWARETYR H:33 , TYR H:35 , TRP H:105 , FUC H:223 , NDG H:225 , FUC H:226 , HIS L:31 , HOH L:1016BINDING SITE FOR RESIDUE GAL H 224
3AC3SOFTWAREASP H:31 , TYR H:32 , TYR H:33 , ASN H:210 , LYS H:212 , FUC H:223 , GAL H:224 , FUC H:226 , HOH H:259 , HOH H:330BINDING SITE FOR RESIDUE NDG H 225
4AC4SOFTWARETYR H:35 , THR H:100 , GLY H:103 , SER H:104 , TRP H:105 , GAL H:224 , NDG H:225 , HOH H:236 , HOH H:237 , TYR L:37BINDING SITE FOR RESIDUE FUC H 226
5AC5SOFTWARESER L:9 , THR L:90 , TYR L:92 , GLN L:105 , GLY L:106BINDING SITE FOR RESIDUE GOL L 1001

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:202
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:152 -Pro H:153
5Gln H:154 -Pro H:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S3K)

(-) Exons   (0, 0)

(no "Exon" information available for 1S3K)

(-) 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 d1s3kh1 H:1-119 Immunoglobulin light chain kappa variable domain, VL-kappa                                             d1s3kh2 H:120-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma               SCOP domains
               CATH domains 1s3kH01 H:1-119 Immunoglobulins                                                                                        1s3kH02 H:120-219 Immunoglobulins                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeeeee...eeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s3k H   1 EVQLVESGGGVVQPGRSLRLSCSTSGFTFSDYYMYWVRQAPGKGLEWVAYMSNVGAITDYPDTVKGRFTISRDNSKNTLFLQMDSLRPEDTGVYFCARGTRDGSWFAYWGQGTPVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPQPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 ||    147       157       167       177       187       197       207       217  
                                                                                                                                                             132|                                                                               
                                                                                                                                                              140                                                                               


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1s3kl1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1s3kl2 L:113-216 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1s3kL01 L:1-113 Immunoglobulins                                                                                  1s3kL02 L:114-216 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..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s3k L   1 DIQMTQSPSSLSASVGDRVTITCRSSQRIVHSNGNTYLEWYQQTPGKAPKLLIYKVSNRFSGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCFQGSHVPFTFGQGTKLQITRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    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 1S3K)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1S3K)

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