3U6D Hydrolase Dna date Oct 12, 2011
title Mutm Set 1 Gpgo
authors R.J.Sung, M.Zhang, Y.Qi, G.L.Verdine
compound source
Molecule: Formamidopyrimidine-Dna Glycosylase
Chain: A
Ec: 3.2.2.23
Engineered: Yes
Mutation: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Agpgptpapgpaptpcpcpcpgpap 3');
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna (5'-D(Tpgpcpgptpcpgp(8og)Pgpap(Tx) Pcptpapcpc)-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Dna
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.188 93.541 104.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.87 Å
ligand 08Q, 8OG, ZN enzyme Hydrolase E.C.3.2.2.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSEQUENCE-DEPENDENT STRUCTURAL VARIATION IN DNA UNDERGOING INTRAHELICAL INSPECTION BY MUTM., Sung RJ, Zhang M, Qi Y, Verdine GL, J Biol Chem. 2012 Mar 30. PMID:22465958
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (115 Kb) [Save to disk]
  • Biological Unit Coordinates (3u6d.pdb1.gz) 110 Kb
  • LPC: Ligand-Protein Contacts for 3U6D
  • CSU: Contacts of Structural Units for 3U6D
  • Structure Factors (479 Kb)
  • Retrieve 3U6D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U6D from S2C, [Save to disk]
  • Re-refined 3u6d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U6D 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 3U6D
  • 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 3U6D, from MSDmotif at EBI
  • Fold representative 3u6d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u6d_A] [3u6d_B] [3u6d] [3u6d_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3U6D: [Fapy_DNA_glyco] [H2TH ] by SMART
  • Other resources with information on 3U6D
  • Community annotation for 3U6D at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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