4YD1 Ternary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dUMPNPP date
authors Moon, A.F., Gosavi, R.A., Kunkel, T.A., Pedersen, L.C., Bebenek, K.
compound source
symmetry
R_factor
R_Free 0.190
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.75
ligand CL, DUP, EDO, GOL, MG, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCreative template-dependent synthesis by human polymerase mu., Moon AF, Gosavi RA, Kunkel TA, Pedersen LC, Bebenek K, Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4530-6. doi:, 10.1073/pnas.1505798112. Epub 2015 Aug 3. PMID:26240373
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (4yd1.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 4YD1
  • CSU: Contacts of Structural Units for 4YD1
  • Structure Factors (445 Kb)
  • Retrieve 4YD1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YD1 from S2C, [Save to disk]
  • Re-refined 4yd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YD1 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 4YD1
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yd1] [4yd1_A] [4yd1_D] [4yd1_T] [4yd1_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4YD1: [POLXc ] by SMART
    • Other resources with information on 4YD1
  • Community annotation for 4YD1 at PDBWiki (http://pdbwiki.org)

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