2ASD	Transferase Dna	date	Aug 23, 2005
title	Oxog-Modified Insertion Ternary Complex
authors	O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geac D.J.Patel
compound		source
Molecule: 5'-D(Gpgptptpgpgpaptpgpgptpap(Ddg))- Chain: D, H Engineered: Yes Other_details: Primer Strand (Dideoxy-Terminated At 3'-End)		Synthetic: Yes
Molecule: 5'-D(Cptapapcp(8og) Pcptpapcpcpaptpcpcpapapcpc)-3'; Chain: E, J Engineered: Yes Other_details: Oxog-Modified Template Strand		Synthetic: Yes
Molecule: Dna Polymerase Iv Chain: A, B Synonym: Pol Iv, Dpo4 Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Sulfolobus Solfataricus Organism_taxid: 2287 Gene: Dbh, Dpo4 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3)-Ril (Stratagene) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-28a
symmetry	Space Group: P 1 21 1	R_factor 0.225 R_Free 0.253
crystal cell	length a length b length c angle alpha angle beta angle gamma 75.955 101.109 84.124 90.00 97.14 90.00
method	X-Ray Diffraction	resolution	1.95 Å
ligand	8OG, CA, DCP, DDG	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion., Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ, PLoS Biol. 2006 Jan 3;4(1):e11. PMID:16379496

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (151 Kb) [Save to disk] Biological Unit Coordinates (2asd.pdb1.gz) 73 Kb Biological Unit Coordinates (2asd.pdb2.gz) 73 Kb LPC: Ligand-Protein Contacts for 2ASD CSU: Contacts of Structural Units for 2ASD Likely Quarternary Molecular Structure file(s) for 2ASD Structure Factors (1651 Kb) Retrieve 2ASD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2ASD from S2C, [Save to disk] Re-refined 2asd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2ASD 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 2ASD

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 2ASD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2asd_D] [2asd] [2asd_B] [2asd_A] [2asd_H] [2asd_J] [2asd_E] SWISS-PROT database: [Q97W02] Domain organization of [DPO42_SULSO] by SWISSPFAM

Other resources with information on 2ASD

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

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Images from IMB Jena Image Library of Biological Macromolecules.

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