3LK9 Lyase,Transferase Dna date Jan 27, 2010
title Dna Polymerase Beta With A Gapped Dna Substrate And Dtmp(Cf2
authors M.Zibinsky, G.K.Surya Prakash, T.G.Upton, B.A.Kashemirov, C.E.Mc K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.
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: Pwl11

Molecule: Dna (5'-D(Cpcpgpapcpapgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-3')
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.198 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
49.960 79.800 55.050 90.00 108.46 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CL, MG, NA, TFF enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSynthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid., Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA, Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15693-8. Epub 2010 Aug 19. PMID:20724659
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (3lk9.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 3LK9
  • CSU: Contacts of Structural Units for 3LK9
  • Structure Factors (113 Kb)
  • Retrieve 3LK9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LK9 from S2C, [Save to disk]
  • Re-refined 3lk9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LK9 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 3LK9
  • 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 3LK9, from MSDmotif at EBI
  • Fold representative 3lk9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lk9] [3lk9_T] [3lk9_P] [3lk9_D] [3lk9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3LK9: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3LK9
  • Community annotation for 3LK9 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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