3JPN Transferase Dna date Sep 04, 2009
title Ternary Complex Of Dna Polymerase Beta With A Dideoxy Termin Primer And 2'-Deoxyguanosine 5'-Beta, Gamma-Dichloro Methyl Triphosphate
authors V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodm C.E.Mckenna
compound source
Molecule: Dna Polymerase Beta
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Gpcptpgpaptpgpcpgp(Doc))-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Cpcpgpapcpcpgpcpgpcpaptpcpapg
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.190 R_Free 0.242
length a length b length c angle alpha angle beta angle gamma
50.650 80.110 55.480 90.00 107.93 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand CL, DOC, G2C, MG enzyme Transferase E.C. BRENDA

Primary referenceHalogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues., Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE, J Am Chem Soc. 2010 May 13. PMID:20465217
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (3jpn.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 3JPN
  • CSU: Contacts of Structural Units for 3JPN
  • Structure Factors (181 Kb)
  • Retrieve 3JPN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JPN from S2C, [Save to disk]
  • Re-refined 3jpn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3JPN 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 3JPN
  • 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 3JPN, from MSDmotif at EBI
  • Fold representative 3jpn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jpn_T] [3jpn] [3jpn_P] [3jpn_A] [3jpn_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3JPN: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3JPN
  • Community annotation for 3JPN 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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