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(-) Description

Title :  ANTI-LEWIS Y FAB FRAGMENT WITH LEWIS Y ANTIGEN IN THE PRESENCE OF ZINC IONS
 
Authors :  W. Farrugia, A. M. Scott, P. A. Ramsland
Date :  22 Oct 08  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Immunoglobulin Fold, Beta Barrel, Humanized Antibody, Antigen Binding Fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Farrugia, A. M. Scott, P. A. Ramsland
A Possible Role For Metallic Ions In The Carbohydrate Cluster Recognition Displayed By A Lewis Y Specific Antibody.
Plos One V. 4 E7777 2009
PubMed-ID: 19901987  |  Reference-DOI: 10.1371/JOURNAL.PONE.0007777

(-) Compounds

Molecule 1 - HU3S193 FAB, LIGHT CHAIN
    Chains: L, A
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: NS0 MURINE MYELOMA CELLS
    Expression System Taxid: 10090
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 2 - HU3S193 FAB, HEAVY CHAIN
    Chains: H, B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: NS0 MURINE MYELOMA CELLS
    Expression System Taxid: 10090
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:1 , HIS H:170 , ASN L:142 , ASN L:143BINDING SITE FOR RESIDUE ZN L 220
2AC2SOFTWAREASP A:190 , ASP L:190 , HIS L:194BINDING SITE FOR RESIDUE ZN L 221
3AC3SOFTWAREGAL H:224 , NDG H:225 , HIS L:31 , ASN L:33BINDING SITE FOR RESIDUE FUC H 223
4AC4SOFTWARETYR H:33 , TYR H:35 , TRP H:105 , FUC H:223 , NDG H:225 , FUC H:226 , HIS L:31 , PHE L:101 , HOH L:223BINDING SITE FOR RESIDUE GAL H 224
5AC5SOFTWAREASP H:31 , TYR H:32 , TYR H:33 , FUC H:223 , GAL H:224 , FUC H:226BINDING SITE FOR RESIDUE NDG H 225
6AC6SOFTWARETYR H:35 , THR H:100 , GLY H:103 , SER H:104 , TRP H:105 , GAL H:224 , NDG H:225 , HOH H:233 , TYR L:37BINDING SITE FOR RESIDUE FUC H 226
7AC7SOFTWAREASN A:142 , ASN A:143 , HIS B:170 , GLU H:1 , HOH H:227BINDING SITE FOR RESIDUE ZN A 220
8AC8SOFTWAREASP A:190 , HIS A:194BINDING SITE FOR RESIDUE ZN A 221
9AC9SOFTWAREHOH B:647 , HOH B:648 , HOH B:649BINDING SITE FOR RESIDUE GOL B 605

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:93
2A:139 -A:199
3A:219 -B:222
4B:22 -B:96
5B:146 -B:202
6H:22 -H:96
7H:146 -H:202
8L:23 -L:93
9L:139 -L:199

(-) Cis Peptide Bonds  (10, 10)

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
6Ser A:7 -Pro A:8
7Val A:99 -Pro A:100
8Tyr A:145 -Pro A:146
9Phe B:152 -Pro B:153
10Gln B:154 -Pro B:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EYV)

(-) 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 A from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3eyva1 A:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d3eyva2 A:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3eyvA02 A:114-219 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eyv A   1 DIQMTQSPSSLSASVGDRVTITCRSSQRIVHSNGNTYLEWYQQTPGKAPKLLIYKVSNRFSGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCFQGSHVPFTFGQGTKLQITRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains d3eyvb1 B:1-119 Immunoglobulin light chain kappa variable domain, VL-kappa                                             d3eyvb2 B:120-222 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 3eyvB01 B:1-119 Immunoglobulins                                                                                        3eyvB02 B:120-222 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeeee...eeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eyv B   1 EVQLVESGGGVVQPGRSLRLSCSTSGFTFSDYYMYWVRQAPGKGLEWVAYMSNVGAITDYPDTVKGRFTISRDNSKNTLFLQMDSLRPEDTGVYFCARGTRDGSWFAYWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPQPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3eyvh1 H:1-119 Immunoglobulin light chain kappa variable domain, VL-kappa                                             d3eyvh2 H:120-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 3eyvH01 H:1-119 Immunoglobulins                                                                                        3eyvH02 H:120-219 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eyv H   1 EVQLVESGGGVVQPGRSLRLSCSTSGFTFSDYYMYWVRQAPGKGLEWVAYMSNVGAITDYPDTVKGRFTISRDNSKNTLFLQMDSLRPEDTGVYFCARGTRDGSWFAYWGQGTPVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPQPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 219
                                    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:216
                                                                                                                                                                                                                                                        
               SCOP domains d3eyvl1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d3eyvl2 L:113-216 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------3eyvL02 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....eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eyv 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)
  - → 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  (4, 8)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3EYV)

(-) Related Entries Specified in the PDB File

1s3k COMPLEX OF HU3S193 FAB AND LEWIS Y IN THE ABSENCE OF ZINC IONS