1Q3F Hydrolase Dna date Jul 29, 2003
title Uracil Dna Glycosylase Bound To A Cationic 1-Aza-2'-Deoxyrib Containing Dna
authors M.A.Bianchet, L.A.Seiple, Y.L.Jiang, Y.Ichikawa, L.M.Amzel, J.T.S
compound source
Molecule: 5'-D(Tpgptp(Nri)Paptpcptpt)-3'
Chain: B
Engineered: Yes
Other_details: 1-Aza-2'-Deoxyribose-Containing Dna
Synthetic: Yes

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

Synthetic: Yes

Molecule: Uracil-Dna Glycosylase
Chain: A
Synonym: Udg
Ec: 3.2.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ung Or Dgu Or Ung15
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.640 65.890 99.410 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand NRI, PO4, URA enzyme Hydrolase E.C.3.2.2 BRENDA
related structures by homologous chain: 1OKB, 1SSP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceElectrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase., Bianchet MA, Seiple LA, Jiang YL, Ichikawa Y, Amzel LM, Stivers JT, Biochemistry 2003 Nov 4;42(43):12455-60. PMID:14580190
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1q3f.pdb1.gz) 49 Kb
  • LPC: Ligand-Protein Contacts for 1Q3F
  • CSU: Contacts of Structural Units for 1Q3F
  • Likely Quarternary Molecular Structure file(s) for 1Q3F
  • Retrieve 1Q3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q3F from S2C, [Save to disk]
  • View 1Q3F 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 1Q3F
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1Q3F, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q3fa_, 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: [1q3f] [1q3f_C] [1q3f_A] [1q3f_B]
  • SWISS-PROT database: [P13051]
  • Domain organization of [UNG_HUMAN] by SWISSPFAM
  • Domains found in 1Q3F: [UDG] [UreE_C ] by SMART
  • Other resources with information on 1Q3F
  • Community annotation for 1Q3F 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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