Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  TANKYRASE 2 IN COMPLEX WITH METHYL 4-(4-OXOCHROMEN-2-YL)BENZOATE
 
Authors :  M. Narwal, T. Haikarainen, L. Lehtio
Date :  05 Jun 13  (Deposition) - 30 Oct 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Ligand Complex, Diphtheria Toxin Like Fold, Transferase, Adp- Ribosylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Narwal, J. Koivunen, T. Haikarainen, E. Obaji, O. E. Legala, H. Venkannagari, P. Joensuu, T. Pihlajaniemi, L. Lehtio
Discovery Of Tankyrase Inhibiting Flavones With Increased Potency And Isoenzyme Selectivity.
J. Med. Chem. V. 56 7880 2013
PubMed-ID: 24116873  |  Reference-DOI: 10.1021/JM401463Y

(-) Compounds

Molecule 1 - TANKYRASE-2
    ChainsA, B
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainROSETTA 2(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL FRAGMENT, UNP RESIDUES 946-1113
    GeneTNKS2, PARP5B, TANK2, TNKL
    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
 
Molecule 2 - TANKYRASE-2
    ChainsC, D
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainROSETTA 2(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL FRAGMENT, UNP RESIDUES 1114-1162
    GeneTNKS2, PARP5B, TANK2, TNKL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1F082Ligand/IonMETHYL 4-(4-OXO-4H-CHROMEN-2-YL)BENZOATE
2GOL1Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1F081Ligand/IonMETHYL 4-(4-OXO-4H-CHROMEN-2-YL)BENZOATE
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1F081Ligand/IonMETHYL 4-(4-OXO-4H-CHROMEN-2-YL)BENZOATE
2GOL-1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:1031 , GLY A:1032 , PHE A:1035 , ALA A:1049 , TYR A:1050 , TYR A:1060 , PHE A:1061 , ALA A:1062 , LYS A:1067 , SER A:1068 , TYR A:1071 , ILE A:1075 , HOH A:1339 , HOH A:1420 , GLU C:1138BINDING SITE FOR RESIDUE F08 A 1201
2AC2SOFTWAREARG A:977 , HIS A:979 , ARG A:980 , LYS A:1067 , GLN A:1070 , HOH A:1387 , HOH C:1313BINDING SITE FOR RESIDUE SO4 A 1202
3AC3SOFTWAREASN A:990 , ARG A:991 , HOH A:1390 , PRO C:1160 , GLU C:1161 , HOH C:1306BINDING SITE FOR RESIDUE SO4 A 1203
4AC4SOFTWARECYS A:1081 , HIS A:1084 , CYS A:1089 , CYS A:1092BINDING SITE FOR RESIDUE ZN A 1204
5AC5SOFTWAREPRO C:1129 , SER C:1130 , VAL C:1131 , GLY C:1133BINDING SITE FOR RESIDUE GOL C 1201
6AC6SOFTWARECYS B:1081 , HIS B:1084 , CYS B:1089 , CYS B:1092BINDING SITE FOR RESIDUE ZN B 1201
7AC7SOFTWAREHIS B:1031 , GLY B:1032 , PHE B:1035 , ALA B:1049 , TYR B:1050 , TYR B:1060 , ALA B:1062 , LYS B:1067 , SER B:1068 , TYR B:1071 , ILE B:1075 , HOH B:1395 , GLU D:1138BINDING SITE FOR RESIDUE F08 B 1202
8AC8SOFTWAREARG B:977 , HIS B:979 , ARG B:980 , LYS B:1067 , GLN B:1070 , HOH B:1375 , HOH D:1311BINDING SITE FOR RESIDUE SO4 B 1203
9AC9SOFTWAREASN B:990 , ARG B:991 , HOH B:1323 , PRO D:1160 , GLU D:1161BINDING SITE FOR RESIDUE SO4 D 1201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L31)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L31)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L31)

(-) Exons   (0, 0)

(no "Exon" information available for 4L31)

(-) Sequences/Alignments

Asymmetric 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:161
                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhh.hhhhh.........eeee.hhhhhhh...hhhhh...............eeeeeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4l31 A  952 GTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSA 1112
                                   961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111 

Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh.hhhhh.........eeee.hhhhhhh...hhhhh...............eeeeeeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4l31 B  952 GTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAM 1113
                                   961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111  

Chain C from PDB  Type:PROTEIN  Length:47
                                                                                
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee........eeee.hhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                4l31 C 1115 MAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPE 1161
                                  1124      1134      1144      1154       

Chain D from PDB  Type:PROTEIN  Length:47
                                                                                
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee........eeee.hhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                4l31 D 1115 MAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPE 1161
                                  1124      1134      1144      1154       

   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 4L31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L31)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L31)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    F08  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4l31)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  4l31
    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 4bjc 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 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

4bs4
4hki TANKYRASE 2 IN COMPLEX WITH FLAVONE
4kzl
4kzq
4kzu
4l09
4l0b
4l0i
4l0s
4l0t
4l0v
4l10
4l2f
4l2g
4l2k
4l32
4l33
4l34