Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HUMAN TDG IN A POST-REACTIVE COMPLEX WITH 5-HYDROXYMETHYLURACIL (5HMU)
 
Authors :  H. Hashimoto, S. Hong, A. S. Bhagwat, X. Zhang, X. Cheng
Date :  19 Jun 12  (Deposition) - 19 Sep 12  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Base Excision Repair, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, S. Hong, A. S. Bhagwat, X. Zhang, X. Cheng
Excision Of 5-Hydroxymethyluracil And 5-Carboxylcytosine By The Thymine Dna Glycosylase Domain: Its Structural Basis An Implications For Active Dna Demethylation.
Nucleic Acids Res. V. 40 10203 2012
PubMed-ID: 22962365  |  Reference-DOI: 10.1093/NAR/GKS845

(-) Compounds

Molecule 1 - G/T MISMATCH-SPECIFIC THYMINE DNA GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1056
    Expression System Taxid: 562
    Fragment: HUMAN TDG GLYCOSYLASE DOMAIN, UNP RESIDUES 111-308
    Gene: TDG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: THYMINE-DNA GLYCOSYLASE
 
Molecule 2 - DNA (28-MER)
    Chains: C
    Engineered: YES
    Other Details: DNA OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES
 
Molecule 3 - DNA (29-MER)
    Chains: D
    Engineered: YES
    Other Details: DNA OLIGONUCLEOTIDE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AAB1Mod. Nucleotide2'-DEOXY-RIBOFURANOSE-5'-MONOPHOSPHATE
2HMU1Ligand/Ion5-HYDROXYMETHYL URACIL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:138 , ILE A:139 , ASN A:140 , TYR A:152 , ASN A:157 , ASN A:230 , SER A:271 , HOH A:529 , AAB D:17BINDING SITE FOR RESIDUE HMU A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FNC)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FNC)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...........eeeee...hhhhhhhh........hhhhhhhhh.......hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhh.........ee..........eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fnc A 110 SFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERN 305
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299      


Chain C from PDB  Type:DNA  Length:28
                                                            
                 4fnc C   1 CAGCTCTGTACGTGAGCAGTGGACAGCT  28
                                    10        20        


Chain D from PDB  Type:DNA  Length:29
                                                             
                 4fnc D   1 AGCTGTCCACTGCTCAxGTACAGAGCTGT  29
                                    10      | 20         
                                           17-AAB
   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  (0, 0)

(no "SCOP Domain" information available for 4FNC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AAB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HMU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fnc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4fnc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TDG_HUMAN | Q13569
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.29
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TDG_HUMAN | Q13569
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TDG_HUMAN | Q13569: 1wyw 2d07 2rba 3ufj 3uo7 3uob 4jgc 4xeg 4z3a 4z47 4z7b 4z7z 5cys 5ff8 5hf7 5jxy 5t2w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4FNC)