2DDG	Hydrolase Dna	date	Jan 28, 2006
title	Crystal Structure Of Uracil-Dna Glycosylase In Complex With Containing Dna
authors	H.Kosaka, N.Nakagawa, R.Masui, J.Hoseki, S.Kuramitsu, Riken Struc Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: 5'-D(Aptpgptptpgpcp(D1p)Ptptpapgptp Chain: C Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Gpgpapcptpapapgpgpcpapapcpa)-3 Chain: D Engineered: Yes		Synthetic: Yes
Molecule: Uracil-Dna Glycosylase Chain: A Ec: 3.2.2.- Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8 Gene: Ttudgb Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11a
symmetry	Space Group: C 2 2 21	R_factor 0.218 R_Free 0.240
crystal cell	length a length b length c angle alpha angle beta angle gamma 68.927 150.174 93.408 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	2HP, ACT, EOH, GOL, ORP, SF4	enzyme	Hydrolase E.C.3.2.2 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Crystal structure of family 5 uracil-DNA glycosylase bound to DNA., Kosaka H, Hoseki J, Nakagawa N, Kuramitsu S, Masui R, J Mol Biol. 2007 Nov 2;373(4):839-50. Epub 2007 Aug 21. PMID:17870091

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk] Biological Unit Coordinates (2ddg.pdb1.gz) 53 Kb LPC: Ligand-Protein Contacts for 2DDG CSU: Contacts of Structural Units for 2DDG Likely Quarternary Molecular Structure file(s) for 2DDG Structure Factors (503 Kb) Retrieve 2DDG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DDG from S2C, [Save to disk] Re-refined 2ddg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DDG 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 2DDG

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 2DDG, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2ddg_A] [2ddg_D] [2ddg] [2ddg_C] SWISS-PROT database: [Q5SJ65] Domain organization of [Q5SJ65_THET8] by SWISSPFAM Domains found in 2DDG: [UDG] [UreE_C ] by SMART

Other resources with information on 2DDG

Community annotation for 2DDG at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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