2KQD Lyase date Nov 04, 2009
title First Pbz Domain Of Human Aplf Protein In Complex With Ribofuranosyladenosine
authors D.Neuhaus, S.Eustermann, C.Brockmann, J.Yang
compound source
Molecule: Aprataxin And Pnk-Like Factor
Chain: A
Fragment: Sequence Database Residues 363-451, Pbz-Type 1 Domain;
Synonym: Apurinic-Apyrimidinic Endonuclease Aplf, Pnk And Aptx-Like Fha Domain-Containing Protein, Xrcc1-Interacting Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aplf, C2orf13, Palf, Xip1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Pgex-6p-1
methodSolution NMR
ligand ADN, RIB, ZN enzyme Lyase E.C. BRENDA
Primary referenceSolution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose)., Eustermann S, Brockmann C, Mehrotra PV, Yang JC, Loakes D, West SC, Ahel I, Neuhaus D, Nat Struct Mol Biol. 2010 Feb;17(2):241-3. Epub 2010 Jan 24. PMID:20098424
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (145 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 2KQD
  • CSU: Contacts of Structural Units for 2KQD
  • Original NMR restraints for 2KQD from PDB
  • Retrieve 2KQD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2KQD from S2C, [Save to disk]
  • View 2KQD 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 2KQD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2KQD, from MSDmotif at EBI
  • Fold representative 2kqd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2kqd] [2kqd_A]
  • SWISS-PROT database: [Q8IW19]
  • Domain organization of [APLF_HUMAN] by SWISSPFAM
  • Other resources with information on 2KQD
  • Community annotation for 2KQD 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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