5J2K Transferase Dna date Mar 29, 2016
title Ternary Complex Crystal Structure Of Dna Polymerase Beta Wit Mismatch At The Primer Terminus
authors V.K.Batra, S.H.Wilson
compound source
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

Molecule: Template Strand
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Primer Strand
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Downstream Primer Strand
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.220 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.820 80.170 55.380 90.00 107.86 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CL, DUP, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism., Batra VK, Beard WA, Pedersen LC, Wilson SH, Structure. 2016 Sep 13. pii: S0969-2126(16)30238-6. doi:, 10.1016/j.str.2016.08.006. PMID:27642161
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (5j2k.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 5J2K
  • CSU: Contacts of Structural Units for 5J2K
  • Structure Factors (316 Kb)
  • Retrieve 5J2K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5J2K from S2C, [Save to disk]
  • Re-refined 5j2k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5J2K 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 5J2K
  • 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 5j2k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5j2k_A] [5j2k] [5j2k_T] [5j2k_D] [5j2k_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5J2K: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5J2K
  • Community annotation for 5J2K at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science