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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANTI-HIS TAG ANTIBODY 3D5 SINGLE-CHAIN FRAGMENT (SCFV) IN COMPLEX WITH A OLIGOHISTIDINE PEPTIDE
 
Authors :  M. Kaufmann, P. Lindner, A. Honegger, K. Blank, M. Tschopp, G. Capitani, A. Plueckthun, M. G. Gruetter
Date :  17 Jan 02  (Deposition) - 15 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  H,L,M,P
Keywords :  Immunoglobulin Domains, Single Chain Antibody/Antigen Complex, His Tag Recognition, Scfv, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kaufmann, P. Lindner, A. Honegger, K. Blank, M. Tschopp, G. Capitani, A. Pluckthun, M. G. Grutter
Crystal Structure Of The Anti-His Tag Antibody 3D5 Single-Chain Fragment Complexed To Its Antigen.
J. Mol. Biol. V. 318 135 2002
PubMed-ID: 12054774  |  Reference-DOI: 10.1016/S0022-2836(02)00038-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-HIS TAG ANTIBODY 3D5 VARIABLE LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAK1HMUT1+2_NOM
    Expression System Strain: SB536
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MONOCLONAL ANTIBODY 3D5
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - PEPTIDE LINKER
    Chains: M
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAK1HMUT1+2_NOM
    Expression System Strain: SB536
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MONOCLONAL ANTIBODY 3D5
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: THE PEPTIDE LINKER CONNECTS THE VARIABLE LIGHT CHAIN AND THE VARIABLE HEAVY CHAIN.
 
Molecule 3 - ANTI-HIS TAG ANTIBODY 3D5 VARIABLE HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAK1HMUT1+2_NOM
    Expression System Strain: SB536
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MONOCLONAL ANTIBODY 3D5
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 4 - OLIGOHISTIDINE PEPTIDE ANTIGEN
    Chains: P
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHETIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : HLMP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KTR)

(-) Sites  (0, 0)

(no "Site" information available for 1KTR)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:23 -H:106
2L:23 -L:106

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:135 -Pro L:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:114
 aligned with Q924R5_MOUSE | Q924R5 from UniProtKB/TrEMBL  Length:139

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
         Q924R5_MOUSE     1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSRATLTVDKPSSTAYMQLSSLTSEDSAVYYCALLAEAYWGQGTLVTVSA 114
               SCOP domains d1ktrh_ H: Immunoglobulin heavy chain variable domain, VH                                                          SCOP domains
               CATH domains 1ktrH00 H:1-149 Immunoglobulins                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee....ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1ktr H   1 QVQLQQSGPEDVKPGASVKISCKASGYTFTDYYMNWVKQSPGKGLEWIGDINPNNGGTSYNQKFKGRATLTVDKSSSTAYMELRSLTSEDSSVYYCESQSGAYWGQGTTVTVSA 149
                                  ||11        21     || 32||      47        57   ||   70        80        90       100       110|      145    
                                  7|                27|  33|                    61|                                          110|             
                                   9                 29   39                     65                                           136             


Chain L from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d1ktrl_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 1ktrL00 L:1-149 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1ktr L   1 DILMTQTPSSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKR 149
                                    10        20      ||32  ||    43        53    ||  71        81  ||    93       103       136       146   
                                                     27|   35|                   58|               84|                     111|              
                                                      30    37                    67                87                      135              


Chain M from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 1ktr M 150 GG 151


Chain P from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1ktr P   3 HHHH   6
   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  (2, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Cis Peptide Bonds
    Thr L:7 - Pro L:8   [ RasMol ]  
    Val L:135 - Pro L:136   [ RasMol ]  
 

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