1EMH Hydrolase Dna date Mar 16, 2000
title Crystal Structure Of Human Uracil-Dna Glycosylase Bound To U Substrate-Containing Dna
authors S.S.Parikh, G.Slupphaug, H.E.Krokan, G.M.Blackburn, J.A.Tainer
compound source
Molecule: Dna (5'-D(Tpgptp(P2u)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
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 0.216 R_Free 0.233
length a length b length c angle alpha angle beta angle gamma
48.655 64.815 94.964 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand P2U enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1AKZ, 1OKB

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 (1emh.pdb1.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 1EMH
  • CSU: Contacts of Structural Units for 1EMH
  • Likely Quarternary Molecular Structure file(s) for 1EMH
  • Retrieve 1EMH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1EMH from S2C, [Save to disk]
  • View 1EMH 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 1EMH
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1EMH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1emha_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1emh from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1emh_C] [1emh_B] [1emh] [1emh_A]
  • SWISS-PROT database: [P13051]
  • Domain organization of [UNG_HUMAN] by SWISSPFAM
  • Domains found in 1EMH: [UDG] [UreE_C ] by SMART
  • Other resources with information on 1EMH
  • Community annotation for 1EMH 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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