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 PARP14 (ARTD8)-MACRO DOMAIN 1 IN COMPLEX WITH ADENOSINE-5-DIPHOSPHORIBOSE
 
Authors :  T. Karlberg, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra, R A. M. Edwards, T. Ekblad, S. Flodin, A. Flores, S. Graslund, T. Kotenyo E. Kouznetsova, M. Moche, P. Nordlund, T. Nyman, C. Persson, A. Sehic, A. G. Thorsell, L. Tresaugues, E. Wahlberg, J. Weigelt, M. Welin, H. Sc Structural Genomics Consortium (Sgc)
Date :  04 Jan 11  (Deposition) - 09 Feb 11  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics Consortium, Sgc, Adp-Ribose Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. Forst, T. Karlberg, N. Herzog, A. G. Thorsell, A. Gross, K. L. Feijs, P. Verheugd, P. Kursula, B. Nijmeijer, E. Kremmer, H. Kleine, A. G. Ladurner, H. Schuler, B. Luscher
Recognition Of Mono-Adp-Ribosylated Artd10 Substrates By Artd8 Macrodomains.
Structure V. 21 462 2013
PubMed-ID: 23473667  |  Reference-DOI: 10.1016/J.STR.2012.12.019

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 14
    Chains: A
    EC Number: 2.4.2.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3) R3 PRARE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MACRO DOMAIN 1, RESIDUES 708-898
    Gene: BAL2, KIAA1268, PARP14
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARP-14, B AGGRESSIVE LYMPHOMA PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:5 , HOH A:14 , HOH A:28 , HOH A:54 , ALA A:822 , ASN A:824 , LYS A:828 , GLY A:831 , GLY A:832 , LEU A:833 , ALA A:834 , SER A:922 , SER A:923 , GLY A:924 , VAL A:925 , PHE A:926 , ASP A:961 , HOH A:980BINDING SITE FOR RESIDUE APR A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q6Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q6Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q6Z)

(-) 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:185
 aligned with PAR14_HUMAN | Q460N5 from UniProtKB/Swiss-Prot  Length:1801

    Alignment length:187
                                   801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       
          PAR14_HUMAN   792 CFSRTVLAPGVVLIVQQGDLARLPVDVVVNASNEDLKHYGGLAAALSKAAGPELQADCDQIVKREGRLLPGNATISKAGKLPYHHVIHAVGPRWSGYEAPRCVYLLRRAVQLSLCLAEKYKYRSIAIPAISSGVFGFPLGRCVETIVSAIKENFQFKKDGHCLKEIYLVDVSEKTVEAFAEAVKTVF 978
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------Macro-3q6zA01 A:820-898                                                        -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeeee.........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.......eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhh....--....eeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q6z A 792 CFSRTVLAPGVVLIVQQGDLARLPVDVVVNASNEDLKHYGGLAAALSKAAGPELQADCDQIVKREGRLLPGNATISKAGKLPYHHVIHAVGPRWSGYEAPRCVYLLRRAVQLSLCLAEKYKYRSIAIPAISSGVFGFPLGRCVETIVSAIKENFQFKK--HCLKEIYLVDVSEKTVEAFAEAVKTVF 978
                                   801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       | -|      961       971       
                                                                                                                                                                                       949  |                          
                                                                                                                                                                                          952
   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 3Q6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q6Z)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: MACRO (14)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAR14_HUMAN | Q460N5)
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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

 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
    APR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3q6z)
 

(-) 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
  3q6z
    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
  PAR14_HUMAN | Q460N5
    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
  PAR14_HUMAN | Q460N5
    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
        PAR14_HUMAN | Q460N5: 3goy 3q71 3se2 3smi 3smj 3vfq 4abk 4abl 4d86 4f1l 4f1q 4py4 5lxp 5lyh 5nqe 5v7t 5v7w

(-) Related Entries Specified in the PDB File

3q71 3v2b 3vfq 4abk 4abl 4d86