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(-) Description

Title :  ANTIBODY 64M-2 FAB COMPLEXED WITH DTT(6-4)TT
 
Authors :  H. Yokoyama, R. Mizutani, Y. Satow, K. Sato, Y. Komatsu, E. Ohtsuka, O. N
Date :  15 Nov 01  (Deposition) - 15 Nov 02  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Protein-Dna Complex, Dna Photoproduct, Immunoglobulin, Immune System- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yokoyama, R. Mizutani, Y. Satow, K. Sato, Y. Komatsu, E. Ohtsuka, O. Nikaido
Structure Of The Dna (6-4) Photoproduct Dtt(6-4)Tt In Complex With The 64M-2 Antibody Fab Fragment Implies Increased Antibody-Binding Affinity By The Flanking Nucleotides.
Acta Crystallogr. , Sect. D V. 68 232 2012
PubMed-ID: 22349224  |  Reference-DOI: 10.1107/S0907444912000327
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*TP*(64T)P*TP*T)-3'
    Chains: A
    Engineered: YES
    Other Details: THE CHAIN WAS SYNTHESIZED BY COUPLING THYMIDINES TO BOTH SIDES OF DT(6-4)T WHICH WAS PURIFIED FROM ULTRAVIOLET-RADIATED DTPT.
    Synthetic: YES
 
Molecule 2 - ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (LIGHT CHAIN)
    Cell Line: HYBRIDOMA
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 3 - ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-2 FAB (HEAVY CHAIN)
    Cell Line: HYBRIDOMA
    Chains: H
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
164T1Mod. Nucleotide5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP L:1 , HIS L:189BINDING SITE FOR RESIDUE NI L 213

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KEG)

(-) 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:DNA  Length:4
                                     
                1keg A    1 TtTT    4
                             |  
                             |  
                             2-64T


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains d1kegh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1kegh2 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 1kegH01 H:1-113 Immunoglobulins                                                                                         1kegH02 H:114-226 Immunoglobulins                                                             -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eeeeeeee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1keg H    1 EVQLQQSGTVLARPGASVKMSCKASGYSFTSFWMHWVKQRPGQGLEWIGTIYPGNSDTSYNQKFKGKAKLTAVTSASTAYMEVSSLTNEDSAVYYCTRRSGYKYYALDYWGQGTSVTVSSAKTTAPSVYPLAPVCGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123    || 139       149    |||164    || 175    || 187       198 ||   |210       220  ||  
                                                                              52A                            82A||               100I||                         128|                154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                100J|                          135                 156||     171       183           198 ||  208             226  
                                                                                                               82C                 100K                                               157|                               200|                       
                                                                                                                                                                                       162                                202                       


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains d1kegl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1kegl2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1kegL01 L:1-108 Immunoglobulins                                                                                 -1kegL02 L:110-209 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1keg L    1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSLVPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C||      35        45        55        65        75        85        95|      106       116       126       136       146       156       166       176       186       196       206      
                                                     27A||||                                                                  95|                                                                                                                   
                                                      27B|||                                                                   97                                                                                                                   
                                                       27C||                                                                                                                                                                                        
                                                        27D|                                                                                                                                                                                        
                                                         27E
   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 1KEG)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
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    Thr L:7 - Pro L:8   [ RasMol ]  
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    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  GCAA_MOUSE | P01863
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 Related Entries

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

UniProtKB/Swiss-Prot
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1kn2 1kn4 1kno 1mh5 1mnu 1mpa 1ob1 1pg7 1uyw 1yec 1yef 1yeg 1yeh 1yei 1yej 1yek 2ipu 2mpa 2r0w 2r0z 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3oz9 3zo0 4f37 5vaa

(-) Related Entries Specified in the PDB File

1ehl 1EHL CONTAINS THE SAME PROTEIN.