2V9W	Transferase	date	Aug 27, 2007
title	Complex Structure Of Sulfolobus Solfataricus Dpo4 And Dna Du Containing A Hydrophobic Thymine Isostere 2,4-Difluorotolue Nucleotide In The Template Strand
authors	A.Irimia, P.S.Pallan, M.Egli
compound		source
Molecule: Dna Polymerase Iv Chain: A, B Synonym: Pol Iv Ec: 2.7.7.7 Engineered: Yes Other_details: Dpo4		Organism_scientific: Sulfolobus Solfataricus Organism_taxid: 273057 Strain: P2 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet22b-Dpo4-Nhis
Molecule: 5'-D(Gpgpgpgpgpapapgpgpap Cptpg)-3' Chain: C, E Engineered: Yes Other_details: 13-Mer Primer		Synthetic: Yes
Molecule: 5'-D(Tptpcpapgpdftpapgptpcpcp Tptpcpcpcpcpc)-3'; Chain: D, F Engineered: Yes Other_details: 18-Mer Template		Synthetic: Yes
symmetry	Space Group: P 1 21 1	R_factor 0.218 R_Free 0.290
crystal cell	length a length b length c angle alpha angle beta angle gamma 52.704 186.744 52.730 90.00 110.06 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	CA, DCT, DFT	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structure and Activity of Y-class DNA Polymerase DPO4 from Sulfolobus solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene., Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M, J Biol Chem. 2007 Dec 14;282(50):36421-33. Epub 2007 Oct 18. PMID:17951245

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk] Biological Unit Coordinates (2v9w.pdb1.gz) 71 Kb Biological Unit Coordinates (2v9w.pdb2.gz) 71 Kb LPC: Ligand-Protein Contacts for 2V9W CSU: Contacts of Structural Units for 2V9W Likely Quarternary Molecular Structure file(s) for 2V9W Structure Factors (129 Kb) Retrieve 2V9W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2V9W from S2C, [Save to disk] Re-refined 2v9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2V9W 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 2V9W

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 2V9W, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2v9w_A] [2v9w_F] [2v9w_C] [2v9w] [2v9w_D] [2v9w_B] [2v9w_E] SWISS-PROT database: [Q97W02] Domain organization of [DPO42_SULSO] by SWISSPFAM

Other resources with information on 2V9W

Community annotation for 2V9W at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---