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(-) Description

Title :  ANTIBODY 64M-5 FAB IN COMPLEX WITH A DOUBLE-STRANDED DNA (6-4) PHOTOPRODUCT
 
Authors :  H. Yokoyama, R. Mizutani, Y. Satow
Date :  30 Jul 12  (Deposition) - 27 Mar 13  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Protein-Dna Complex, Dna (6-4) Photoproduct, Immunoglobulin, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yokoyama, R. Mizutani, Y. Satow
Structure Of A Double-Stranded Dna (6-4) Photoproduct In Complex With The 64M-5 Antibody Fab
Acta Crystallogr. , Sect. D V. 69 504 2013
PubMed-ID: 23519658  |  Reference-DOI: 10.1107/S0907444912050007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-5 FAB (LIGHT CHAIN)
    Chains: L
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: BALB/C
 
Molecule 2 - ANTI-(6-4) PHOTOPRODUCT ANTIBODY 64M-5 FAB (HEAVY CHAIN)
    Chains: H
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: BALB/C
 
Molecule 3 - DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY) P*AP*TP*GP*GP*AP*CP*GP*G)-3')
    Chains: A
    Engineered: YES
    Other Details: DNA WITH (6-4) PHOTOPRODUCT
    Synthetic: YES
 
Molecule 4 - DNA (5'- D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3')
    Chains: B
    Engineered: YES
    Other Details: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
15PY1Mod. Nucleotide1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE
264T1Mod. Nucleotide5-HYDROXY-THYMIDINE-5'-MONOPHOSPHATE
3NCO1Ligand/IonCOBALT HEXAMMINE(III)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:11 , ASP H:56 , THR H:57 , THR H:58BINDING SITE FOR RESIDUE NCO H 301

(-) 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:200 -Pro H:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VW3)

(-) Exons   (0, 0)

(no "Exon" information available for 3VW3)

(-) 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:18
                                                   
                3vw3 A    1 GCGAGTGAttATGGACGG   18
                                    10        
                                    9-64T     
                                    10-5PY    


Chain B from PDB  Type:DNA  Length:18
                                                   
                3vw3 B    1 CCCGTCCATAATCACTCG   18
                                    10        


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee.....eeeee...eeeee..........eee............eeeeeeee.....eeee........eee...ee....eeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3vw3 H    1 EVQLQQSGTVLARPGASVKMSCKASGYTFTNYWMHWIKQRPGQGLEWIGTIYPGNSDTTYSQKFKGKAKLTAVTSTSTAYMELSSLTNEDSAVYYCSRRNYGSSYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTSTWPSETVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123      |136       146       157|      172       184       199||     210       220  ||  
                                                                              52A                            82A||               100I||                           130|||               154|||    169|      180|      192||||                  223|  
                                                                                                              82B|                100J|                            133||                156||     171       183       196|||                   226  
                                                                                                               82C                 100K                             134|                 157|                          199||                        
                                                                                                                                                                     136                  162                           200|                        
                                                                                                                                                                                                                         202                        


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeeee........eeeeeeeeeehhhhhhh.eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3vw3 L    2 VLMTQTPLSLPVSLGDQASISCRSSQNIVHSNGYTYLEWYLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFRGSHVPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    11        21      |27D|       36        46        56        66        76        86        97       107       117       127       137       147       157       167       177       187       197       207     
                                                    27A||||                                                                  95|                                                                                                                   
                                                     27B|||                                                                   97                                                                                                                   
                                                      27C||                                                                                                                                                                                        
                                                       27D|                                                                                                                                                                                        
                                                        27E
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3VW3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VW3)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Cis Peptide Bonds
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 Related Entries

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(-) Related Entries Specified in the PDB File

1ehl THE RELATED ANTIBODY FAB IN COMPLEX WITH DNA (6-4) PHOTOPRODUCT
1keg THE RELATED ANTIBODY FAB IN COMPLEX WITH DNA (6-4) PHOTOPRODUCT