4YD1 Transferase Dna date Feb 20, 2015
title Ternary Complex Of Human Dna Polymerase Mu With 2-Nt Gapped Substrate And An Incoming Nonhydrolyzable Dumpnpp
authors A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek
compound source
Molecule: Dna-Directed Dnarna Polymerase Mu
Chain: A
Synonym: Pol Mu,Terminal Transferase
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polm, Polmu
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgexm

Molecule: Dna (5'-D(Cpgpgpcpapaptpapcpg)-3')
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Cpgptpa)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgpcpcpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.163 R_Free 0.190
length a length b length c angle alpha angle beta angle gamma
60.259 69.042 116.988 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand CL, DUP, EDO, GOL, MG, NA enzyme Transferase E.C. BRENDA

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] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (4yd1.pdb1.gz) 136 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
  • 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
  • Fold representative 4yd1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science