3KJD Transferase date Nov 03, 2009
title Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In C With An Inhibitor Abt-888
authors T.Karlberg, P.Schutz, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Co A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Jo I.Johansson, A.Kallas, T.Kotenyova, A.Kotzsch, P.Kraulis, T.K.Ni M.Moche, P.Nordlund, T.Nyman, C.Persson, A.K.Roos, M.I.Siponen, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wisniewska, H.Schuler, Structural Genomics Consortium (Sgc)
compound source
Molecule: Poly [Adp-Ribose] Polymerase 2
Chain: A, B
Fragment: Catalytic Domain
Synonym: Parp-2, Nad(+) Adp-Ribosyltransferase 2, Poly[Adp- Synthetase 2, Padprt-2, Hparp-2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adprt2, Adprtl2, Parp2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)R2 Prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 1 21 1
R_factor 0.179 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
58.134 134.611 58.314 90.00 117.68 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand 78P, GOL enzyme Transferase E.C. BRENDA
A, B

Primary referenceCrystal structure of the catalytic domain of human PARP2 in complex with PARP inhibitor ABT-888., Karlberg T, Hammarstrom M, Schutz P, Svensson L, Schuler H, Biochemistry. 2010 Feb 16;49(6):1056-8. PMID:20092359
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (3kjd.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3kjd.pdb2.gz) 64 Kb
  • LPC: Ligand-Protein Contacts for 3KJD
  • CSU: Contacts of Structural Units for 3KJD
  • Structure Factors (432 Kb)
  • Retrieve 3KJD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KJD from S2C, [Save to disk]
  • Re-refined 3kjd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KJD in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3KJD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3KJD, from MSDmotif at EBI
  • Fold representative 3kjd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kjd] [3kjd_B] [3kjd_A]
  • SWISS-PROT database: [Q9UGN5]
  • Domain organization of [PARP2_HUMAN] by SWISSPFAM
  • Other resources with information on 3KJD
  • Community annotation for 3KJD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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