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 :  HUMAN ARTD3 (PARP3) - CATALYTIC DOMAIN IN COMPLEX WITH INHIBITOR ME0354
 
Authors :  T. Karlberg, A. G. Thorsell, A. E. G. Lindgren, T. Ekblad, S. Spjut, C. D. Andersson, J. Weigelt, A. Linusson, M. Elofsson, H. Schuler
Date :  30 Aug 12  (Deposition) - 19 Jun 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Nad, Adp-Ribose, Parp3, Artd3, Artd Transferase Domain, Adp- Ribosylation, Transferase-Transferase Inhibitor Complex, Transferase, Adp-Ribosylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. E. G. Lindgren, T. Karlberg, A. G. Thorsell, M. Hesse, S. Spjut, T. Ekblad, C. D. Andersson, A. F. Pinto, J. Weigelt, M. O. Hottiger, A. Linusson, M. Elofsson, H. Schuler
Parp Inhibitor With Selectivity Toward Adp-Ribosyltransferase Artd3/Parp3
Acs Chem. Biol. V. 8 1698 2013
PubMed-ID: 23742272  |  Reference-DOI: 10.1021/CB4002014

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 3
    Chains: A
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 178-532
    Gene: PARP3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARP-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
15ME1Ligand/Ion3-(4-OXO-3,4-DIHYDROQUINAZOLIN-2-YL)-N-[(1R)-1-(PYRIDIN-2-YL)ETHYL]PROPANAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:287 , ASP A:291 , HIS A:384 , GLY A:385 , TYR A:414 , SER A:422 , TYR A:425 , GLU A:514 , DMS A:602 , HOH A:703 , HOH A:736 , HOH A:849 , HOH A:860BINDING SITE FOR RESIDUE 5ME A 601
2AC2SOFTWAREHIS A:384 , GLY A:398 , LEU A:399 , ARG A:400 , 5ME A:601 , HOH A:838BINDING SITE FOR RESIDUE DMS A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GV2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GV2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GV2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GV2)

(-) Exons   (0, 0)

(no "Exon" information available for 4GV2)

(-) 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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4gv2a1 A:176-321 automated matches                                                                                                            d4gv2a2 A:322-532 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.ee.hhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeeeeeeee...hhhhhhh......eeeeeee.hhhhhhhhhhhh..............eee..hhhhhhh....eee..eeeeeeeeeeee...eeee...............eeee...eee.hhhheeeee..eeeee....eee.hhhh.......eeee.hhh.eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gv2 A 176 SMKRVQPCSLDPATQKLITNIFSKEMFKNTMALMDLDVKKMPLGKLSKQQIARGFEALEALEEALKDGGQSLEELSSHFYTVIPHNFGHSQPPPINSPELLQAKKDMLLVLADIELAQALQAVSEQEKTVEEVPHPLDRDYQLLKCQLQLLDSGAPEYKVIQTYLEQTGSNHRCPTLQHIWKVNQEGEEDRFQAHSKLGNRKLLWHGTNMAVVAAILTSGLRIMPHSGGRVGKGIYFASENSKSAGYVIGMKCGAHHVGYMFLGEVALGREHHINTDNPSLKSPPPGFDSVIARGHTEPDPTQDTELELDGQQVVVPQGQPVPCPEFSSSTFSQSEYLIYQESQCRLRYLLEVH 532
                                   185       195       205       215       225       235     ||248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528    
                                                                                           241|                                                                                                                                                                                                                                                                                               
                                                                                            245
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GV2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GV2)

(-) Gene Ontology  (20, 20)

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
    5ME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gv2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4gv2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PARP3_HUMAN | Q9Y6F1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.30
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PARP3_HUMAN | Q9Y6F1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PARP3_HUMAN | Q9Y6F1: 2eoc 3c49 3c4h 3ce0 3fhb 4gv0 4gv4 4l6z 4l70 4l7l 4l7n 4l7o 4l7p 4l7r 4l7u

(-) Related Entries Specified in the PDB File

4gv0 THE SAME PROTEIN COMPLEXED WITH ME0355
4gv4 THE SAME PROTEIN COMPLEXED WITH ME0328