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 :  MOUSE TDP2 REACTION PRODUCT (5'-PHOSPHORYLATED DNA)-CA2+ COMPLEX
 
Authors :  M. J. Schellenberg, R. S. Williams
Date :  07 Mar 16  (Deposition) - 27 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase/Dna, Dna Repair, Endonuclease/Exonuclease/Phosphatase (Eep) Domain, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Schellenberg, L. Perera, C. N. Strom, C. A. Waters, B. Monian, C. D. Appel, C. K. Vilas, J. G. Williams, D. A. Ramsden, R. S. Williams
Reversal Of Dna Damage Induced Topoisomerase 2 Dna-Protein Crosslinks By Tdp2.
Nucleic Acids Res. V. 44 3829 2016
PubMed-ID: 27060144  |  Reference-DOI: 10.1093/NAR/GKW228

(-) Compounds

Molecule 1 - TYROSYL-DNA PHOSPHODIESTERASE 2
    ChainsA, B
    EC Number3.1.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GeneTDP2, TTRAP
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymTYR-DNA PHOSPHODIESTERASE 2,5'-TYROSYL-DNA PHOSPHODIESTERASE,5'-TYR-DNA PHOSPHODIESTERASE,TRAF AND TNF RECEPTOR- ASSOCIATED PROTEIN
 
Molecule 2 - DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3')
    ChainsC, D
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GOL1Ligand/IonGLYCEROL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:132 , GLU A:162 , HOH A:525 , HOH A:542 , HOH A:585 , DC D:1 , HOH D:106binding site for residue CA A 401
2AC2SOFTWAREPRO A:208 , HOH A:511binding site for residue PEG A 402
3AC3SOFTWAREASP B:132 , GLU B:162 , HOH B:506 , HOH B:529 , HOH B:569 , DC C:1 , HOH C:104binding site for residue CA B 401
4AC4SOFTWARECYS B:149 , TYR B:153 , VAL B:345 , GLY B:346 , LEU B:347binding site for residue EPE B 402
5AC5SOFTWAREPHE B:209 , PRO B:210 , ASN B:211 , GLU B:246 , ARG B:249 , THR B:253binding site for residue GOL B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5INQ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5INQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5INQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5INQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5INQ)

(-) 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:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee...eeeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5inq A 116 KGLEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365     

Chain B from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..eeeee......eeeeeee....eeeeeeeee........eeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh......eeeeeee...hhhhhhhh.......eehhhhh..hhhhh..ee.............ee..eeeeee.....eeeeeeeee...............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5inq B 123 TISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL 370
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        

Chain C from PDB  Type:DNA  Length:9
                                         
                 5inq C   1 CCGAATTCG   9

Chain D from PDB  Type:DNA  Length:9
                                         
                 5inq D   1 CCGAATTCG   9

   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 5INQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5INQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5INQ)

(-) Gene Ontology  (19, 19)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5inq)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5inq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TYDP2_MOUSE | Q9JJX7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.4.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TYDP2_MOUSE | Q9JJX7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TYDP2_MOUSE | Q9JJX74gyz 4gz0 4gz1 4gz2 4puq 5ht2 5ink 5inl 5inm 5inn 5inp 5j3z 5j42

(-) Related Entries Specified in the PDB File

4gz1 4GZ1 HAS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT METAL ION
5ink
5inl
5inm
5inn
5ino
5inp