5T14 Transferase Dna date Aug 17, 2016
title Dna Polymerase Kappa Extending Beyond A Bulky Major Benzo[A] Adduct
authors V.K.Jha, H.Ling
compound source
Molecule: Dna Polymerase Kappa
Chain: A, B
Synonym: Dinb Protein,Dinp
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polk, Dinb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna
Chain: C, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Dna
Chain: D, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 21 21 21
R_factor 0.204 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.250 128.820 167.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand DZ4, MG, PGE, VKJ enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa., Jha V, Ling H, DNA Repair (Amst). 2016 Nov 19. pii: S1568-7864(16)30359-7. doi:, 10.1016/j.dnarep.2016.11.001. PMID:27894903
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (5t14.pdb1.gz) 82 Kb
  • Biological Unit Coordinates (5t14.pdb2.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 5T14
  • CSU: Contacts of Structural Units for 5T14
  • Structure Factors (1920 Kb)
  • Retrieve 5T14 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5T14 from S2C, [Save to disk]
  • Re-refined 5t14 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5T14 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 5T14
  • 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 5t14 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5t14_P] [5t14_C] [5t14_D] [5t14] [5t14_A] [5t14_B] [5t14_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5T14
  • Community annotation for 5T14 at PDBWiki (http://pdbwiki.org)

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