6NKS Transcription Dna date Jan 07, 2019
title Ternary Complex Crystal Structure Of K289m Variant Of Dna Po Beta With Beta-Gamma Chf Analog Of Dgtp
authors V.K.Batra, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t3

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.189 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
50.607 80.327 55.391 90.00 108.13 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand CL, DOC, GFH, MG, NA enzyme Transferase E.C. BRENDA

Primary referenceRevealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography., Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH, Biochemistry. 2020 Mar 3;59(8):955-963. doi: 10.1021/acs.biochem.9b01072. Epub, 2020 Feb 12. PMID:31999437
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (6nks.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 6NKS
  • CSU: Contacts of Structural Units for 6NKS
  • Structure Factors (229 Kb)
  • Retrieve 6NKS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6NKS from S2C, [Save to disk]
  • View 6NKS 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 6NKS
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6nks from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6nks_P] [6nks_T] [6nks_D] [6nks_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6NKS
  • Community annotation for 6NKS at PDBWiki (http://pdbwiki.org)

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