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 :  CRYSTAL STRUCTURE OF HUMAN TANKYRASE 2 IN COMPLEX WITH RUCAPARIB
 
Authors :  T. Haikarainen, M. Narwal, L. Lehtio
Date :  18 Apr 13  (Deposition) - 11 Dec 13  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Protein-Ligand Complex, Diphtheria Toxin Like Fold, Adp- Ribosylation, Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Haikarainen, M. Narwal, P. Joensuu, L. Lehtio
Evaluation And Structural Basis For The Inhibition Of Tankyrases By Parp Inhibitors
Acs Med. Chem. Lett. V. 5 18 2014
PubMed-ID: 24900770  |  Reference-DOI: 10.1021/ML400292S

(-) Compounds

Molecule 1 - TANKYRASE-2
    ChainsA
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA 2
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL FRAGMENT, RESIDUES 946-1162
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTANK2, ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 6, ARTD6, POLY [ADP-RIBOSE] POLYMERASE 5B, TNKS-2, TRF1-INTERACTING ANKYRIN-RELATED ADP-RIBOSE POLYMERASE 2, TANKYRASE II, TANKYRASE-LIKE PROTEIN, TANKYRASE-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1RPB1Ligand/IonRUCAPARIB
2SO42Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1031 , GLY A:1032 , TYR A:1060 , PHE A:1061 , ALA A:1062 , LYS A:1067 , SER A:1068 , TYR A:1071 , GLU A:1138 , HOH A:2089BINDING SITE FOR RESIDUE RPB A2162
2AC2SOFTWAREARG A:977 , HIS A:979 , ARG A:980 , LYS A:1067 , GLN A:1070 , ASN A:1132 , HOH A:2028 , HOH A:2067BINDING SITE FOR RESIDUE SO4 A2163
3AC3SOFTWAREARG A:977 , HIS A:979 , ARG A:980 , LYS A:1067 , GLN A:1070 , ASN A:1132 , HOH A:2028 , HOH A:2067BINDING SITE FOR RESIDUE SO4 A2163
4AC4SOFTWAREASN A:990 , ARG A:991 , MET A:1158 , ARG A:1159 , PRO A:1160 , GLU A:1161 , HOH A:2035BINDING SITE FOR RESIDUE SO4 A2164
5AC5SOFTWARECYS A:1081 , HIS A:1084 , CYS A:1089 , CYS A:1092BINDING SITE FOR RESIDUE ZN A2165

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PARP_CATALYTICPS51059 PARP catalytic domain profile.TNKS2_HUMAN959-1164  1A:959-1161

(-) Exons   (0, 0)

(no "Exon" information available for 4BJC)

(-) 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:197
 aligned with TNKS2_HUMAN | Q9H2K2 from UniProtKB/Swiss-Prot  Length:1166

    Alignment length:210
                                   961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161
         TNKS2_HUMAN    952 GTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPE 1161
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh.....--------..eeee.hhhhhhh...hhhhh...............eeeeeeeee...eeeeee-----.......eeeeee........eeee.hhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PARP_CATALYTIC  PDB: A:959-1161 UniProt: 959-1164                                                                                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4bjc A  952 GTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERH--------AGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFS-----HSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPE 1161
                                   961       971       981       991      1001      1011      1021      1031      1041      |  -     |1061      1071      1081      1091      1101      1111     |1121      1131      1141      1151      1161
                                                                                                                         1048     1057                                                  1111  1117                                            

   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 4BJC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TNKS2_HUMAN | Q9H2K2)
molecular function
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:1904357    negative regulation of telomere maintenance via telomere lengthening    Any process that stops, prevents or reduces the frequency, rate or extent of telomere maintenance via telomere lengthening.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:1904355    positive regulation of telomere capping    Any process that activates or increases the frequency, rate or extent of telomere capping.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    GO:0070213    protein auto-ADP-ribosylation    The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein.
    GO:0070198    protein localization to chromosome, telomeric region    Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0000242    pericentriolar material    A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

 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
    RPB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 4bjc)
 

(-) 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
  4bjc
    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
  TNKS2_HUMAN | Q9H2K2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.30
    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
  TNKS2_HUMAN | Q9H2K2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TNKS2_HUMAN | Q9H2K22y0i 3kr7 3kr8 3mhj 3mhk 3p0n 3p0p 3p0q 3twq 3twr 3tws 3twt 3twu 3twv 3tww 3twx 3u9h 3u9y 3ua9 3w51 4avu 4avw 4bfp 4bj9 4bjb 4bs4 4bu3 4bu5 4bu6 4bu7 4bu8 4bu9 4bua 4bud 4bue 4buf 4bui 4bus 4but 4buu 4buv 4buw 4bux 4buy 4hki 4hkk 4hkn 4hl5 4hlf 4hlg 4hlh 4hlk 4hlm 4hmh 4hyf 4iue 4j1z 4j21 4j22 4j3l 4j3m 4kzl 4kzq 4kzu 4l09 4l0b 4l0i 4l0s 4l0t 4l0v 4l10 4l2f 4l2g 4l2k 4l31 4l32 4l33 4l34 4m7b 4pml 4pnl 4pnm 4pnn 4pnq 4pnr 4pns 4pnt 4tju 4tjw 4tjy 4tk0 4tk5 4tkf 4tkg 4tki 4ufu 4ufy 4uhg 4ui3 4ui4 4ui5 4ui6 4ui7 4ui8 4uvl 4uvn 4uvo 4uvp 4uvs 4uvt 4uvu 4uvv 4uvw 4uvx 4uvy 4uvz 4ux4 4w5i 4z68 5adq 5adr 5ads 5adt 5aeh 5aku 5akw 5al1 5al2 5al3 5al4 5al5 5bxo 5bxu 5c5p 5c5q 5c5r 5dcz 5fpf 5fpg 5jrt

(-) Related Entries Specified in the PDB File

4bj9 CRYSTAL STRUCTURE OF HUMAN TANKYRASE 2 IN COMPLEX WITH EB-47
4bjb CRYSTAL STRUCTURE OF HUMAN TANKYRASE 2 IN COMPLEX WITH PJ-34