5CP2 Transferase Dna date Jul 21, 2015
title Human Dna Polymerase Lambda L431a Mutant- Apoenzyme And Comp 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 0.206 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.876 83.876 396.363 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.36 Å
ligand SO4 enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (5cp2.pdb1.gz) 42 Kb
  • Biological Unit Coordinates (5cp2.pdb2.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 5CP2
  • CSU: Contacts of Structural Units for 5CP2
  • Structure Factors (558 Kb)
  • Retrieve 5CP2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CP2 from S2C, [Save to disk]
  • Re-refined 5cp2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CP2 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 5CP2
  • 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 5cp2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cp2_B] [5cp2] [5cp2_T] [5cp2_A] [5cp2_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5CP2: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5CP2
  • Community annotation for 5CP2 at PDBWiki (http://pdbwiki.org)

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