1EMJ Hydrolase Dna date Mar 16, 2000
title Uracil-Dna Glycosylase Bound To Dna Containing A 4'-Thio- 2'Deoxyuridine Analog Product
authors S.S.Parikh, G.Walcher, G.D.Jones, G.Slupphaug, H.E.Krokan, G.M.Bl J.A.Tainer
compound source
Molecule: Dna (5'-D(Tpgptp(Asu)Paptpcptpt)-3')
Chain: B
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Uracil-Dna Glycosylase
Chain: A
Ec: 3.2.2.3
Engineered: Yes
Mutation: Yes
Other_details: Mitochondrial Protein

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.228 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.554 64.853 96.010 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ASU, URA enzyme Hydrolase E.C.3.2.2.3 BRENDA
related structures by homologous chain: 1YUO, 2SSP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceUracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects., Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA, Proc Natl Acad Sci U S A 2000 May 9;97(10):5083-8. PMID:10805771
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1emj.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1EMJ
  • CSU: Contacts of Structural Units for 1EMJ
  • Likely Quarternary Molecular Structure file(s) for 1EMJ
  • Retrieve 1EMJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EMJ from S2C, [Save to disk]
  • View 1EMJ 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 1EMJ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1EMJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1emja_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1emj_A] [1emj_B] [1emj_C] [1emj]
  • SWISS-PROT database: [P13051]
  • Domain organization of [UNG_HUMAN] by SWISSPFAM
  • Domains found in 1EMJ: [UDG] [UreE_C ] by SMART
  • Other resources with information on 1EMJ
  • Community annotation for 1EMJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science