2W7P Dna-Binding Protein date Dec 23, 2008
title Structure And Activity Of Bypass Synthesis By Human Dna Polymerase Kappa Opposite The 7,8-Dihydro-8- Oxodeoxyguanosine Adduct
authors A.Irimia, M.Egli
compound source
Molecule: Dna Polymerase Kappa
Chain: A, B
Fragment: Residues 19-526
Synonym: Dinb, Dinp
Ec: 2.7.7.7
Engineered: Yes
Other_details: Human Dna Polymerase Kappa Catalytic Core, Residues 19-526;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polk, Dinb1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbg101

Molecule: 5'-D(Gpgpgpgpgpapapgpgpaptptpc)-3'
Chain: P, E
Other_details: Primer

Synthetic: Yes

Molecule: 5'-D(Tpcpapcp8ogpgpapaptpcpcptp Tpcpcpcpcpc)-3';
Chain: T, F
Other_details: Template

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.236 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
167.829 220.847 119.208 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.71 Å
ligand 8OG, CA, DTP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and functional elucidation of the mechanism promoting error-prone synthesis by human DNA polymerase kappa opposite the 7,8-Dihydro-8-oxo-2'-deoxyguanosine adduct., Irimia A, Eoff RL, Guengerich FP, Egli M, J Biol Chem. 2009 Jun 19. PMID:19542228
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (2w7p.pdb1.gz) 85 Kb
  • Biological Unit Coordinates (2w7p.pdb2.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 2W7P
  • CSU: Contacts of Structural Units for 2W7P
  • Likely Quarternary Molecular Structure file(s) for 2W7P
  • Structure Factors (195 Kb)
  • Retrieve 2W7P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2W7P from S2C, [Save to disk]
  • Re-refined 2w7p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2W7P 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 2W7P
  • 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 2W7P, from MSDmotif at EBI
  • Fold representative 2w7p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2w7p_B] [2w7p] [2w7p_T] [2w7p_E] [2w7p_F] [2w7p_P] [2w7p_A]
  • SWISS-PROT database: [Q9UBT6]
  • Domain organization of [POLK_HUMAN] by SWISSPFAM
  • Other resources with information on 2W7P
  • Community annotation for 2W7P 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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