6NKX Transcription Dna date Jan 07, 2019
title Ternary Complex Crystal Structure Of K289m Variant Of Dna Po Beta With "Hot-Spot Sequence" With Dgtp
authors V.K.Batra, S.H.Wilson
compound source
Molecule: Dna (5'-D(Cpcpgpapapcpapapgpcpaptpcp 3');
Chain: T
Ec: 2.7.7.7
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcptpgpaptpgpcptp(2dt))-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

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

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7,4.2.99.-
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: Tap56
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pwl11
symmetry Space Group: P 1 21 1
R_factor 0.181 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.516 79.884 55.200 90.00 107.99 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand 2DT, CL, DGT, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (6nkx.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 6NKX
  • CSU: Contacts of Structural Units for 6NKX
  • Structure Factors (212 Kb)
  • Retrieve 6NKX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6NKX from S2C, [Save to disk]
  • View 6NKX 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 6NKX
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6nkx_D] [6nkx_T] [6nkx_A] [6nkx_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6NKX
  • Community annotation for 6NKX at PDBWiki (http://pdbwiki.org)

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