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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ANTI-CARCINOEMBRYONIC ANTIGEN MONOCLONAL ANTIBODY T84.66 FV FRAGMENT
 
Authors :  H. Kondo, Y. Nishimura, M. Shiroishi, R. Asano, N. Noro, K. Tsumoto, I. K
Date :  01 Nov 02  (Deposition) - 16 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A (1x),B (1x),H (1x),L (1x)
Keywords :  Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kondo, Y. Nishimura, M. Shiroishi, R. Asano, N. Noro, K. Tsumoto, I. Kumagai
The Crystal Structure Of Anti-Carcinoembryonic Antigen Monoclonal Antibody T84. 66 Fv Fragment
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ANTI-CEA MAB T84.66, LIGHT CHAIN
    Chains: L, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FV FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: T84.66 ANTIBODY
 
Molecule 2 - ANTI-CEA MAB T84.66, HEAVY CHAIN
    Chains: H, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FV FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: T84.66 ANTIBODY

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x): A (1x)B (1x)H (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:33 , ARG B:50 , ASP B:52 , ASN B:54 , ASN B:56 , HOH B:539 , ASN H:28BINDING SITE FOR RESIDUE PO4 B 501
2AC2SOFTWARETYR H:33 , ARG H:50 , ASP H:52 , ASN H:54 , ASN H:56 , HOH H:542BINDING SITE FOR RESIDUE PO4 H 502
3AC3SOFTWAREGLN A:37 , LYS A:45 , PHE A:62 , ASP A:81 , ASP A:82 , HOH A:1207 , HOH A:1237BINDING SITE FOR RESIDUE GOL A 1201
4AC4SOFTWAREGLY L:66 , SER L:67 , ARG L:68 , THR L:69 , ASP L:70BINDING SITE FOR RESIDUE GOL L 1202

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:88
2B:22 -B:92
3H:22 -H:92
4L:23 -L:88

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Asp L:76 -Pro L:77
3Asp L:94 -Pro L:95
4Ser A:7 -Pro A:8
5Asp A:76 -Pro A:77
6Asp A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J05)

(-) Exons   (0, 0)

(no "Exon" information available for 1J05)

(-) 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 A from PDB  Type:PROTEIN  Length:111
 aligned with KV3A8_MOUSE | P01660 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
         KV3A8_MOUSE      1 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPYTFGGGTKLEIK  111
               SCOP domains d1j05a_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                           SCOP domains
               CATH domains 1j05A00 A:1-107 Immunoglobulins                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...........eeeeee......eeeee...ee.......eeee....eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                1j05 A    1 DIVLTQSPASLAVSLGQRATMSCRAGESVDIFGVGFLHWYQQKPGQPPKLLIYRASNLESGIPVRFSGTGSRTDFTLIIDPVEADDVATYYCQQTNEDPYTFGGGTKLEIK  107
                                    10        20       27C|       36        46        56        66        76        86        96       106 
                                                     27A|||                                                                                
                                                      27B||                                                                                
                                                       27C|                                                                                
                                                        27D                                                                                


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q9JL85_MOUSE | Q9JL85 from UniProtKB/TrEMBL  Length:109

    Alignment length:121
                                    1                                                                                              97   98           
                                    |2        12        22        32        42        52        62        72        82        92    |   98       108 
        Q9JL85_MOUSE      - --------AELVKPGASVKLSCTASGFNIEDTYMHWVKQRPEQGLEWIGRIDPATGHSKYDPKFQGKATITSDTSSNTAYLQLSSLTSEDTAVYYCVRRGAVVFD----YWGQGTALTVSS  109
               SCOP domains d1j05b_ B: Immunoglobulin heavy chain variable domain, VH                                                                 SCOP domains
               CATH domains 1j05B00 B:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee...............eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                1j05 B    1 EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNSKYVPKFQGKATITADTSSNTAYLQLTSLTSEDTAVYYCAPFGYYVSDYAMAYWGQGTSVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96     ||102       112 
                                                                              52A                            82A||                101A|||            
                                                                                                              82B|                 101B||            
                                                                                                               82C                  101C|            
                                                                                                                                     101D            


Chain H from PDB  Type:PROTEIN  Length:121
 aligned with Q9JL85_MOUSE | Q9JL85 from UniProtKB/TrEMBL  Length:109

    Alignment length:121
                                    1                                                                                              97   98           
                                    |2        12        22        32        42        52        62        72        82        92    |   98       108 
        Q9JL85_MOUSE      - --------AELVKPGASVKLSCTASGFNIEDTYMHWVKQRPEQGLEWIGRIDPATGHSKYDPKFQGKATITSDTSSNTAYLQLSSLTSEDTAVYYCVRRGAVVFD----YWGQGTALTVSS  109
               SCOP domains d1j05h_ H: Immunoglobulin heavy chain variable domain, VH                                                                 SCOP domains
               CATH domains 1j05H00 H:1-113 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee...............eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                1j05 H    1 EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNSKYVPKFQGKATITADTSSNTAYLQLTSLTSEDTAVYYCAPFGYYVSDYAMAYWGQGTSVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96     ||102       112 
                                                                              52A                            82A||                101A|||            
                                                                                                              82B|                 101B||            
                                                                                                               82C                  101C|            
                                                                                                                                     101D            


Chain L from PDB  Type:PROTEIN  Length:111
 aligned with KV3A8_MOUSE | P01660 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
         KV3A8_MOUSE      1 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPYTFGGGTKLEIK  111
               SCOP domains d1j05l_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                           SCOP domains
               CATH domains 1j05L00 L:1-107 Immunoglobulins                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........ee.eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                1j05 L    1 DIVLTQSPASLAVSLGQRATMSCRAGESVDIFGVGFLHWYQQKPGQPPKLLIYRASNLESGIPVRFSGTGSRTDFTLIIDPVEADDVATYYCQQTNEDPYTFGGGTKLEIK  107
                                    10        20       27C|       36        46        56        66        76        86        96       106 
                                                     27A|||                                                                                
                                                      27B||                                                                                
                                                       27C|                                                                                
                                                        27D
   Legend:   → Mismatch (orange background)
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    → 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  (2, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J05)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,L   (KV3A8_MOUSE | P01660)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain B,H   (Q9JL85_MOUSE | Q9JL85)

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  Q9JL85_MOUSE | Q9JL85
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 Related Entries

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

UniProtKB/Swiss-Prot
        KV3A8_MOUSE | P01660: 1ejo 1i8i 1i8k 1moe 1qfw 2r29 2r69 2r6p 2vl5 3bsz 4nja

(-) Related Entries Specified in the PDB File

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