2DY4	Transferase Dna	date	Sep 06, 2006
title	Crystal Structure Of Rb69 Gp43 In Complex With Dna Containin Glycol
authors	P.Aller, M.A.Rould, M.Hogg, S.S.Wallace, S.Doublie
compound		source
Molecule: 5'-D(Cpgp(Ctg) Pgpgpapaptpgpacpapgpcpcpgpcpg)-3'; Chain: E, G, I, K Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Gpcpgpgpcptpgptcpaptptpcpcpa) Chain: F, H, J, L Engineered: Yes		Synthetic: Yes
Molecule: Dna Polymerase Chain: A, B, C, D Synonym: Gp43 Ec: 2.7.7.7 Engineered: Yes Mutation: Yes		Organism_scientific: Enterobacteria Phage Rb69 Organism_taxid: 12353 Gene: Gp43 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3)
symmetry	Space Group: P 1 21 1	R_factor 0.229 R_Free 0.281
crystal cell	length a length b length c angle alpha angle beta angle gamma 132.612 122.632 168.695 90.00 96.31 90.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	CTG, MSE	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B DNA-directed DNA polymerase ... nuclease activity exonuclease activity 3'-5' exonuclease activity
Primary reference	A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol., Aller P, Rould MA, Hogg M, Wallace SS, Doublie S, Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):814-8. Epub 2007 Jan 8. PMID:17210917

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (646 Kb) [Save to disk] Biological Unit Coordinates (2dy4.pdb1.gz) 166 Kb Biological Unit Coordinates (2dy4.pdb2.gz) 167 Kb Biological Unit Coordinates (2dy4.pdb3.gz) 167 Kb Biological Unit Coordinates (2dy4.pdb4.gz) 159 Kb LPC: Ligand-Protein Contacts for 2DY4 CSU: Contacts of Structural Units for 2DY4 Likely Quarternary Molecular Structure file(s) for 2DY4 Structure Factors (3378 Kb) Retrieve 2DY4 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DY4 from S2C, [Save to disk] Re-refined 2dy4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DY4 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 2DY4

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 2DY4, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dy4] [2dy4_L] [2dy4_A] [2dy4_C] [2dy4_D] [2dy4_E] [2dy4_K] [2dy4_H] [2dy4_I] [2dy4_F] [2dy4_G] [2dy4_J] [2dy4_B] SWISS-PROT database: [Q38087] Domain organization of [DPOL_BPR69] by SWISSPFAM Domain found in 2DY4: [POLBc ] by SMART

Other resources with information on 2DY4

Community annotation for 2DY4 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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