4YD2 Transferase Dna date Feb 20, 2015
title Nicked Complex Of Human Dna Polymerase Mu With 2-Nt Gapped D Substrate
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
Fragment: Unp Residues 134-494
Synonym: Pol Mu,Terminal Transferase
Ec: 2.7.7.7
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(Cpgpgpcpapapt)-3')
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Cpgptpapt)-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 0.212 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.083 68.700 114.977 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.47 Å
ligand CL, NA, PPV enzyme Transferase E.C.2.7.7.7 BRENDA
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] (129 Kb) [Save to disk]
  • Biological Unit Coordinates (4yd2.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 4YD2
  • CSU: Contacts of Structural Units for 4YD2
  • Structure Factors (174 Kb)
  • Retrieve 4YD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YD2 from S2C, [Save to disk]
  • Re-refined 4yd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YD2 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 4YD2
  • 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 4yd2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yd2_P] [4yd2] [4yd2_T] [4yd2_D] [4yd2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4YD2: [POLXc ] by SMART
  • Other resources with information on 4YD2
  • Community annotation for 4YD2 at PDBWiki (http://pdbwiki.org)

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