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 PARP10 (ARTD10), CATALYTIC FRAGMENT IN COMPLEX WITH PARP INHIBITOR VELIPARIB
 
Authors :  T. Karlberg, A. G. Thorsell, H. Schuler
Date :  20 Sep 16  (Deposition) - 11 Jan 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase Domain, Adp-Ribosylation, Parp Inhibitor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. G. Thorsell, T. Ekblad, T. Karlberg, M. Low, A. F. Pinto, L. Tresaugues, M. Moche, M. S. Cohen, H. Schuler
Structural Basis For Potency And Promiscuity In Poly(Adp-Ribose) Polymerase (Parp) And Tankyrase Inhibitors
J. Med. Chem. V. 60 1262 2017
PubMed-ID: 28001384  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00990

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 10
    ChainsA, B
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNIC-BSA4
    Expression System Taxid469008
    Expression System VariantC41
    Expression System Vector TypePLASMID
    GenePARP10
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPARP-10,ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 10, ARTD10

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
178P2Ligand/Ion(2R)-2-(7-CARBAMOYL-1H-BENZIMIDAZOL-2-YL)-2-METHYLPYRROLIDINIUM
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
178P1Ligand/Ion(2R)-2-(7-CARBAMOYL-1H-BENZIMIDAZOL-2-YL)-2-METHYLPYRROLIDINIUM
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
178P1Ligand/Ion(2R)-2-(7-CARBAMOYL-1H-BENZIMIDAZOL-2-YL)-2-METHYLPYRROLIDINIUM

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:887 , GLY A:888 , CYS A:907 , ALA A:911 , TYR A:919 , SER A:927 , TYR A:932 , HOH A:1254 , HOH A:1270binding site for residue 78P A 1101
2AC2SOFTWAREHIS B:887 , GLY B:888 , CYS B:907 , ALA B:911 , TYR B:919 , LEU B:926 , SER B:927 , TYR B:932binding site for residue 78P B 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LX6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:879 -Pro A:880
2Arg B:879 -Pro B:880
3Cys B:907 -Gly B:908

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LX6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LX6)

(-) Exons   (0, 0)

(no "Exon" information available for 5LX6)

(-) 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:191
                                                                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh.hhhhh..........eeee.hhhhhh............eeeeeeee....eee.....................eee.......eeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lx6 A  817 SMNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFARRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHV 1007
                                   826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006 

Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh................eeee.hhhhhh............eeeeeeee....eee.....................eee.......eeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lx6 B  819 NLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFARRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHV 1007
                                   828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998         

   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 5LX6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LX6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LX6)

(-) Gene Ontology  (20, 20)

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
    78P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:879 - Pro A:880   [ RasMol ]  
    Arg B:879 - Pro B:880   [ RasMol ]  
    Cys B:907 - Gly B:908   [ 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
  5lx6
    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
  PAR10_HUMAN | Q53GL7
    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
  PAR10_HUMAN | Q53GL7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PAR10_HUMAN | Q53GL72dhx 3hkv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LX6)