4XA5 Transferase Dna date Dec 12, 2014
title Crystal Structure Of The Pre-Catalytic Ternary Complex Of Dn Polymerase Lambda With A Templating A And An Incoming 8-Oxo
authors M.J.Burak, K.E.Guja, M.Garcia-Diaz
compound source
Molecule: Dna Polymerase Lambda
Chain: A
Synonym: Pol Lambda,Dna Polymerase Beta-2,Pol Beta2,Dna Pol Kappa;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Primer Dna (5'-D(Cpapgptpap(Doc))-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Template Dna (5'-D(Cpgpgpcpapgptpapcptp
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.199 R_Free 0.227
length a length b length c angle alpha angle beta angle gamma
55.967 62.340 141.613 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 8DG, ACT, CAS, DOC, GOL, MG enzyme Transferase E.C. BRENDA

Primary referenceNucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda., Burak MJ, Guja KE, Garcia-Diaz M, Nucleic Acids Res. 2015 Sep 18;43(16):8089-99. doi: 10.1093/nar/gkv760. Epub 2015, Jul 28. PMID:26220180
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (4xa5.pdb1.gz) 124 Kb
  • LPC: Ligand-Protein Contacts for 4XA5
  • CSU: Contacts of Structural Units for 4XA5
  • Structure Factors (721 Kb)
  • Retrieve 4XA5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XA5 from S2C, [Save to disk]
  • Re-refined 4xa5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XA5 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 4XA5
  • 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 4xa5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xa5_P] [4xa5_T] [4xa5_A] [4xa5] [4xa5_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4XA5: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4XA5
  • Community annotation for 4XA5 at PDBWiki (http://pdbwiki.org)

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