1KDH Binary Complex of Murine Terminal Deoxynucleotidyl Transferase with a Primer Single Stranded DNA date
authors Delarue, M., Boule, J.B., Lescar, J., Expert-Bezancon, N., Jourdan, N., Sukumar, N., Rougeon, F., Papanicolaou, C.
compound source
R_Free 0.297
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.00
ligand BRU, MG, NA enzyme
related structures by homologous chain: 1JMS, 1KEJ

Primary referenceCrystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase., Delarue M, Boule JB, Lescar J, Expert-Bezancon N, Jourdan N, Sukumar N, Rougeon F, Papanicolaou C, EMBO J 2002 Feb 1;21(3):427-39. PMID:11823435
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (1kdh.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 1KDH
  • CSU: Contacts of Structural Units for 1KDH
  • Likely Quarternary Molecular Structure file(s) for 1KDH
  • Structure Factors (73 Kb)
  • Retrieve 1KDH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KDH from S2C, [Save to disk]
  • Re-refined 1kdh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KDH 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 1KDH
  • 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
  • 3D motif for 1KDH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kdha1, region A:148-242 [Jmol] [rasmolscript] [script source]
        - Domain d1kdha3, region A:243-302 [Jmol] [rasmolscript] [script source]
        - Domain d1kdha4, region A:303-510 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1kdh] [1kdh_D] [1kdh_A]
  • SWISS-PROT database: [P09838]
  • Domain organization of [TDT_MOUSE] by SWISSPFAM
  • Domain found in 1KDH: [POLXc ] by SMART
  • Other resources with information on 1KDH
  • Community annotation for 1KDH 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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