5W2C Replication date Jun 06, 2017
title Structure Of Human Dna Polymerase Kappa In Complex With Luci Derived Dna Adduct And Incoming Dampnpp
authors V.K.Jha, H.Ling
compound source
Molecule: Dna Polymerase Kappa
Chain: A, B
Fragment: Unp Residues 1-526
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 (5'-D(Pcpgpgpaptpcpgpapc)-3')
Chain: C, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644

Molecule: Dna (5'-D(Cptpaptp(Ldg)Ptpcpgpaptpcpc
Chain: D, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Unidentified
Organism_taxid: 32644
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.709 128.923 167.705 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand
enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa., Yockey O, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L, Chem Res Toxicol. 2017 Oct 3. doi: 10.1021/acs.chemrestox.7b00227. PMID:28972744
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (5w2c.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (5w2c.pdb2.gz) 84 Kb
  • CSU: Contacts of Structural Units for 5W2C
  • Structure Factors (2028 Kb)
  • Retrieve 5W2C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5W2C from S2C, [Save to disk]
  • View 5W2C 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 5W2C
  • 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 5w2c from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5w2c_C] [5w2c_T] [5w2c_P] [5w2c_D] [5w2c_A] [5w2c_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5W2C
  • Community annotation for 5W2C at PDBWiki (http://pdbwiki.org)

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