6CTI Transcription Dna date Mar 23, 2018
title Ternary Complex Crystal Structure Of Dna Polymerase Beta Wit Dideoxy Terminated Primer With Ccl2, Beta, Gamma Dttp Analo
authors V.K.Batra, S.H.Wilson
compound source
Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
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(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 0.177 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.618 79.117 55.407 90.00 107.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand CL, DOC, MG, NA, VT8 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] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (6cti.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 6CTI
  • CSU: Contacts of Structural Units for 6CTI
  • Structure Factors (253 Kb)
  • Retrieve 6CTI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6CTI from S2C, [Save to disk]
  • View 6CTI 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 6CTI
  • 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 6cti from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6cti_D] [6cti_A] [6cti_P] [6cti_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6CTI
  • Community annotation for 6CTI at PDBWiki (http://pdbwiki.org)

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