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 :  HUMAN TANKYRASE-2 IN COMPLEX WITH MACROCYCLISED EXTENDED PEPTIDE CP4N2M3
 
Authors :  W. Xu, G. Fischer, M. Hyvonen, L. Itzhaki
Date :  09 Jun 15  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.33
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Stapled Peptide, Protein-Protein Interaction, Ankyrin-Repeat Domain, Tankyrase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Xu, Y. H. Lau, G. Fischer, A. Chattopadhyay, Y. S. Tan, C. Verma, M. Hyvonen, D. S. Spring, L. S. Itzhaki
Human Tankyrase-2 In Complex With Extended Stapled Peptide Sp4N2M3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TANKYRASE-2
    ChainsA, B
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGST
    Expression System Taxid469008
    Expression System VariantC41
    Expression System Vector TypePLASMID
    FragmentRESIDUES 488-649
    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
    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
    SyntheticYES

 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  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
14XP2Ligand/Ion4,4'-PROPANE-1,3-DIYLBIS(1-METHYL-1H-1,2,3-TRIAZOLE)
2ACE2Mod. Amino AcidACETYL GROUP
3DMS3Ligand/IonDIMETHYL SULFOXIDE
4NH22Mod. Amino AcidAMINO GROUP
5SO46Ligand/IonSULFATE ION
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
14XP1Ligand/Ion4,4'-PROPANE-1,3-DIYLBIS(1-METHYL-1H-1,2,3-TRIAZOLE)
2ACE1Mod. Amino AcidACETYL GROUP
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4NH21Mod. Amino AcidAMINO GROUP
5SO43Ligand/IonSULFATE ION
Biological Unit 2 (5, 8)
No.NameCountTypeFull Name
14XP1Ligand/Ion4,4'-PROPANE-1,3-DIYLBIS(1-METHYL-1H-1,2,3-TRIAZOLE)
2ACE1Mod. Amino AcidACETYL GROUP
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4NH21Mod. Amino AcidAMINO GROUP
5SO43Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:601 , LYS A:602 , LYS A:633 , HOH A:809 , ASN B:626 , HOH B:878binding site for residue SO4 A 701
02AC2SOFTWAREGLU A:576 , LYS A:580 , LYS A:592 , HIS A:614 , ARG A:623 , HOH A:869 , GLN B:613binding site for residue SO4 A 702
03AC3SOFTWAREARG A:538 , VAL A:539 , SER A:540 , LYS A:557 , HOH A:805 , HOH A:825 , HOH A:856 , HOH A:868binding site for residue SO4 A 703
04AC4SOFTWARECYS A:512 , HIS A:548 , HIS B:548binding site for residue DMS A 704
05AC5SOFTWARELYS A:633 , ASP A:634 , HOH A:848 , GLY B:603 , LYS B:604 , TYR B:605 , GLU B:606 , HOH B:811 , HOH B:815 , HOH B:861binding site for residue SO4 B 701
06AC6SOFTWARELYS B:592 , GLN B:613 , HIS B:614 , ARG B:623 , HOH B:806binding site for residue SO4 B 702
07AC7SOFTWAREASN B:537 , ARG B:538 , VAL B:539 , SER B:540 , LYS B:557 , HOH B:802 , HOH B:825binding site for residue SO4 B 703
08AC8SOFTWARETYR B:605 , LYS B:609 , ASP B:624 , GLY B:625 , HOH B:827binding site for residue DMS B 704
09AC9SOFTWARELYS B:555 , ASP B:556 , GLY B:559binding site for residue DMS B 705
10AD1SOFTWAREASP A:589 , TRP A:591 , PHE A:593 , GLU A:598 , HOH A:879 , ASP B:634 , THR B:637 , GLU C:2 , HOH C:207binding site for Di-peptide ACE C 0 and ARG C 1
11AD2SOFTWARETYR A:569 , HIS A:571 , LYS A:602 , HOH A:837 , GLU B:491 , ARG B:494 , ALA C:7 , 4XP C:100 , HOH C:204 , HOH C:206binding site for Di-peptide GLU C 8 and NH2 C 9
12AD3SOFTWARETYR A:569 , HIS A:571 , LYS A:602 , HOH A:837 , GLU B:491 , ARG B:494 , ALA C:7 , 4XP C:100 , HOH C:204 , HOH C:206binding site for Di-peptide GLU C 8 and NH2 C 9
13AD4SOFTWAREARG A:525 , TYR A:569 , GLU B:506 , THR B:507 , GLU B:523 , GLU C:2 , GLY C:4 , GLY C:6 , ALA C:7 , GLU C:8 , NH2 C:9 , HOH C:202 , HOH C:203binding site for Di-peptide 4XP C 100 and ALA C 3
14AD5SOFTWAREGLY A:535 , TYR A:569 , HIS A:571 , GLU B:506 , THR B:507 , GLU B:523 , ALA C:3 , GLY C:6 , GLU C:8 , NH2 C:9 , HOH C:203 , HOH C:209binding site for Di-peptide 4XP C 100 and ALA C 7
15AD6SOFTWAREASP A:634 , GLY A:635 , THR A:637 , ASP B:589 , TRP B:591 , PHE B:593 , GLU B:598 , GLU D:2 , HOH D:208binding site for Di-peptide ACE D 0 and ARG D 1
16AD7SOFTWAREARG A:494 , TYR B:569 , HIS B:571 , LYS B:602 , HOH B:829 , ALA D:7 , 4XP D:100 , HOH D:201 , HOH D:210 , HOH D:212binding site for Di-peptide GLU D 8 and NH2 D 9
17AD8SOFTWAREARG A:494 , TYR B:569 , HIS B:571 , LYS B:602 , HOH B:829 , ALA D:7 , 4XP D:100 , HOH D:201 , HOH D:210 , HOH D:212binding site for Di-peptide GLU D 8 and NH2 D 9
18AD9SOFTWAREARG A:494 , GLU A:506 , GLU A:523 , GLY B:535 , TYR B:569 , HIS B:571 , ALA D:3 , GLY D:6 , GLU D:8 , NH2 D:9 , HOH D:205 , HOH D:209binding site for Di-peptide 4XP D 100 and ALA D 7
19AE1SOFTWAREARG A:494 , GLU A:506 , GLU A:523 , ARG B:525 , TYR B:569 , GLU D:2 , GLY D:4 , GLY D:6 , ALA D:7 , GLU D:8 , HOH D:203 , HOH D:205 , HOH D:215binding site for Di-peptide 4XP D 100 and ALA D 3

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:487 -Gly B:488

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BXO)

(-) 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:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxo A 487 SGNSEADRQLLEAAKAGDVETVKKLCTVQSVNCRDIEGRQSTPLHFAAGYNRVSVVEYLLQHGADVHAKDKGGLVPLHNACSYGHYEVAELLVKHGAVVNVADLWKFTPLHEAAAKGKYEICKLLLQHGADPTKKNRDGNTPLDLVKDGDTDIQDLLRGD 646
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646

Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhh...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxo B 487 SGNSEADRQLLEAAKAGDVETVKKLCTVQSVNCRDIEGRQSTPLHFAAGYNRVSVVEYLLQHGADVHAKDKGGLVPLHNACSYGHYEVAELLVKHGAVVNVADLWKFTPLHEAAAKGKYEICKLLLQHGADPTKKNRDGNTPLDLVKDGDTDIQDLLRGDAAL 649
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646   

Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5bxo C   0 xREAGDGAEx   9
                            |        9
                            0-ACE    9-NH2

Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5bxo D   0 xREAGDGAEx   9
                            |        9
                            |        9-NH2
                            0-ACE     

   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 5BXO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    4XP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser B:487 - Gly B:488   [ RasMol ]  
 
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
  5bxo
    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 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 5bxu 5c5p 5c5q 5c5r 5dcz 5fpf 5fpg 5jrt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5BXO)