5CHG Transferase Dna date Jul 10, 2015
title Human Dna Polymerase Lambda L431a Mutant- Mgdgtp Binary And With 6 Paired Dna
authors M.S.Liu, M.D.Tsai
compound source
Molecule: Dna Polymerase Lambda
Chain: A, B
Fragment: Unp Residues 242-575
Synonym: Pol Lambda,Dna Polymerase Beta-2,Pol Beta2,Dna Pol Kappa;
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Poll
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 65 2 2
R_factor 0.205 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.893 83.893 398.646 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand DGT, MG, SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Primary referenceStructural Mechanism for the Fidelity Modulation of DNA Polymerase lambda., Liu MS, Tsai HY, Liu XX, Ho MC, Wu WJ, Tsai MD, J Am Chem Soc. 2016 Feb 24;138(7):2389-98. doi: 10.1021/jacs.5b13368. Epub 2016, Feb 11. PMID:26836966
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (5chg.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (5chg.pdb2.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 5CHG
  • CSU: Contacts of Structural Units for 5CHG
  • Structure Factors (319 Kb)
  • Retrieve 5CHG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CHG from S2C, [Save to disk]
  • Re-refined 5chg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CHG 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 5CHG
  • 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 5chg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5chg_A] [5chg_P] [5chg_B] [5chg] [5chg_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CHG: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5CHG
  • Community annotation for 5CHG at PDBWiki (http://pdbwiki.org)

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