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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX BETWEEN AN INHIBITED LLFPG AND A THF CONTAINING DNA
 
Authors :  F. Coste, B. Castaing
Date :  18 Apr 14  (Deposition) - 01 Apr 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Glycosylase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Biela, F. Coste, F. Culard, M. Guerin, S. Goffinont, K. Gasteiger, J. Ciesla, A. Winczura, Z. Kazimierczuk, D. Gasparutto, T. Carell, B. Tudek, B. Castaing
Zinc Finger Oxidation Of Fpg/Nei Dna Glycosylases By 2-Thioxanthine: Biochemical And X-Ray Structural Characterization.
Nucleic Acids Res. V. 42 10748 2014
PubMed-ID: 25143530  |  Reference-DOI: 10.1093/NAR/GKU613

(-) Compounds

Molecule 1 - FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MUTM, FPG
    Organism Scientific: LACTOCOCCUS LACTIS SUBSP. CREMORIS
    Organism Taxid: 1359
    Synonym: FAPY-DNA GLYCOSYLASE,DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE MUTM,AP LYASE MUTM
 
Molecule 2 - DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)- 3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
12ON1Ligand/Ion2-SULFANYL-1,9-DIHYDRO-6H-PURIN-6-ONE
23DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
3GOL1Ligand/IonGLYCEROL

(-) Sites  (0, 0)

(no "Site" information available for 4PDG)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:245 -A:265
2A:248 -A:301

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PDG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PDG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PDG)

(-) Exons   (0, 0)

(no "Exon" information available for 4PDG)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....eeee.hhhhh..hhhhhhhhhh...eeeeeee..eeeeee...eeeeee.....eeeee.........eeeeee....eeeee......eeeeee..hhhhhhhhh...........hhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh..................eeeee..eeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pdg A   1 PELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQGISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFADGQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSALGSTGKMQNELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVCQQK 271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       225       235       245       255       265      
                                                                                                                                                                                                                                                   218|                                               
                                                                                                                                                                                                                                                    224                                               


Chain B from PDB  Type:DNA  Length:14
                                              
                 4pdg B   1 CTCTTTxTTTCTCG  14
                                  | 10    
                                  7-3DR   


Chain C from PDB  Type:DNA  Length:14
                                              
                 4pdg C  15 GCGAGAAACAAAGA  28
                                    24
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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 4PDG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PDG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PDG)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FPG_LACLC | P42371: 1kfv 1nnj 1pji 1pjj 1pm5 1tdz 1xc8 2xzf 2xzu 3c58 4pcz 4pd2 4pdi

(-) Related Entries Specified in the PDB File

4pcz 4pd2 4pdi