2VPW	Oxidoreductase	date	Mar 09, 2008
title	Polysulfide Reductase With Bound Menaquinone
authors	M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamu P.Curmi, S.Iwata
compound		source
Molecule: Thiosulfate Reductase Chain: A, E Synonym: Polysulfide Reductase		Organism_scientific: Thermus Thermophilus Organism_taxid: 262724 Strain: Hb27
Molecule: Nrfc Protein Chain: B, F		Organism_scientific: Thermus Thermophilus Organism_taxid: 262724 Strain: Hb27
Molecule: Hypothetical Membrane Spanning Protein Chain: C, G		Organism_scientific: Thermus Thermophilus Organism_taxid: 262724 Strain: Hb27
symmetry	Space Group: P 21 21 21	R_factor 0.271 R_Free 0.275
crystal cell	length a length b length c angle alpha angle beta angle gamma 115.377 163.580 238.891 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.10 Å
ligand	MGD, MO, MQ7, SF4	enzyme
Gene Ontology	Chain Function Process Component A, E C, G F, B electron transfer activity
Primary reference	Molecular mechanism of energy conservation in polysulfide respiration., Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, Iwata S, Nat Struct Mol Biol. 2008 Jul;15(7):730-7. Epub 2008 Jun 8. PMID:18536726

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (420 Kb) [Save to disk] Biological Unit Coordinates (2vpw.pdb1.gz) 408 Kb LPC: Ligand-Protein Contacts for 2VPW CSU: Contacts of Structural Units for 2VPW Likely Quarternary Molecular Structure file(s) for 2VPW Structure Factors (675 Kb) Retrieve 2VPW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VPW from S2C, [Save to disk] Re-refined 2vpw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VPW 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 2VPW

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 2VPW, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vpw_F] [2vpw_E] [2vpw] [2vpw_A] [2vpw_B] [2vpw_C] [2vpw_G] SWISS-PROT database: [Q72LA4] [Q72LA5] [Q72LA6] Domain organization of [Q72LA4_THET2] [Q72LA5_THET2] [Q72LA6_THET2] by SWISSPFAM Domain found in 2VPW: [Molybdop_Fe4S4 ] by SMART

Other resources with information on 2VPW

Community annotation for 2VPW 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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