3K5M Transferase Dna date Oct 07, 2009
title Crystal Structure Of E.Coli Pol II-Abasic Dna-Ddgtp Lt(-2, 2) Ternary Complex
authors W.Yang, F.Wang
compound source
Molecule: Dna Polymerase II
Chain: A
Synonym: Pol II
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Strain: K-12
Gene: B0060, Dina, Jw0059, Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet28

Molecule: Dna (5'-D(Apgptpcpcptpgp(3dr) Papcpgpcptpapgpgpcpapcpa)-3');
Chain: T
Engineered: Yes
Other_details: Abasic Lt(-2, 2) Template

Synthetic: Yes

Molecule: Dna (5'- D(Gptpgpcpcptpapgpcpgptpapg)-3');
Chain: P
Engineered: Yes
Other_details: Primer

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.243 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
73.109 95.228 144.735 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.04 Å
ligand 3DR, CA, DG3 enzyme Transferase E.C. BRENDA
  • DNA-directed DNA polymerase ...
  • 3'-5'-exodeoxyribonuclease a...

  • Primary referenceStructural insight into translesion synthesis by DNA Pol II., Wang F, Yang W, Cell. 2009 Dec 24;139(7):1279-89. PMID:20064374
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (3k5m.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 3K5M
  • CSU: Contacts of Structural Units for 3K5M
  • Structure Factors (416 Kb)
  • Retrieve 3K5M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3K5M from S2C, [Save to disk]
  • Re-refined 3k5m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3K5M 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 3K5M
  • 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
  • 3D motif for 3K5M, from MSDmotif at EBI
  • Fold representative 3k5m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3k5m_A] [3k5m_P] [3k5m_T] [3k5m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3K5M: [POLBc ] by SMART
  • Other resources with information on 3K5M
  • Community annotation for 3K5M at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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