4U6P Transferase Dna date Jul 29, 2014
title Structural Mechanism Of Error-Free Bypass Of Major Benzo[A]P Adduct By Human Polymerase Kappa
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
Expression_system_strain: Bl21prare
Expression_system_vector_type: Plasmid

Molecule: Dna (5'-D(Pgpcpgpgpaptpcpapc)-3')
Chain: C, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Dna (5'-D(Tpaptpgpgptpgpaptpcpcpgpc)
Chain: D, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 21 21 21
R_factor 0.200 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.150 129.286 167.713 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.59 Å
ligand DCT, MG, PGE enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa., Jha V, Bian C, Xing G, Ling H, Nucleic Acids Res. 2016 Mar 31. pii: gkw204. PMID:27034468
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (4u6p.pdb1.gz) 82 Kb
  • Biological Unit Coordinates (4u6p.pdb2.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 4U6P
  • CSU: Contacts of Structural Units for 4U6P
  • Structure Factors (555 Kb)
  • Retrieve 4U6P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4U6P from S2C, [Save to disk]
  • Re-refined 4u6p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4U6P 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 4U6P
  • 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 4u6p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4u6p] [4u6p_T] [4u6p_P] [4u6p_C] [4u6p_D] [4u6p_A] [4u6p_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4U6P
  • Community annotation for 4U6P at PDBWiki (http://pdbwiki.org)

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