3GDX Transferase Dna date Feb 24, 2009
title Dna Polymerase Beta With A Gapped Dnd Substrate And Dtmp(Cf2
authors S.H.Wilson, V.K.Batra, L.C.Pedersen
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

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

Synthetic: Yes

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

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.208 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.500 79.700 55.300 90.00 107.90 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand 4BD, CL, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAlpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function., Upton TG, Kashemirov BA, McKenna CE, Goodman MF, Prakash GK, Kultyshev R, Batra VK, Shock DD, Pedersen LC, Beard WA, Wilson SH, Org Lett. 2009 May 7;11(9):1883-6. PMID:19351147
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (3gdx.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3GDX
  • CSU: Contacts of Structural Units for 3GDX
  • Likely Quarternary Molecular Structure file(s) for 3GDX
  • Structure Factors (147 Kb)
  • Retrieve 3GDX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GDX from S2C, [Save to disk]
  • Re-refined 3gdx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GDX 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 3GDX
  • 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
  • 3D motif for 3GDX, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gdx_P] [3gdx] [3gdx_A] [3gdx_D] [3gdx_T]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 3GDX: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3GDX
  • Community annotation for 3GDX 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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