6CTR Transcription Dna date Mar 23, 2018
title Ternary Complex Crystal Structure Of Dna Polymerase Beta Wit Dideoxy Terminated Primer With Chf (R & S Isomers), Beta, G Analogue
authors V.K.Batra, S.H.Wilson
compound source
Molecule: Dna (5'-D(Cpcpgpapcpgptpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(2da))-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Pgptpcpgpg)-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

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: Pwl-11
symmetry Space Group: P 1 21 1
R_factor 0.172 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.810 79.712 55.437 90.00 107.72 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand 2DA, CL, DC, F3C, FF4, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMapping functional substrate-enzyme interactions in the pol beta active site through chemical biology: Structural responses to acidity modification of incoming dNTPs., Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH, Biochemistry. 2018 Jun 6. doi: 10.1021/acs.biochem.8b00418. PMID:29874056
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (6ctr.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 6CTR
  • CSU: Contacts of Structural Units for 6CTR
  • Structure Factors (314 Kb)
  • Retrieve 6CTR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CTR from S2C, [Save to disk]
  • View 6CTR 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 6CTR
  • 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 6ctr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ctr_P] [6ctr_A] [6ctr_T] [6ctr_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CTR
  • Community annotation for 6CTR at PDBWiki (http://pdbwiki.org)

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