2VPY	Oxidoreductase	date	Mar 09, 2008
title	Polysulfide Reductase With Bound Quinone Inhibitor, Pentachlorophenol (Pcp)
authors	M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, 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 0.283 R_Free 0.289
crystal cell	length a length b length c angle alpha angle beta angle gamma 117.124 165.194 243.153 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	MGD, MO, PCI, 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] (424 Kb) [Save to disk] Biological Unit Coordinates (2vpy.pdb1.gz) 409 Kb LPC: Ligand-Protein Contacts for 2VPY CSU: Contacts of Structural Units for 2VPY Likely Quarternary Molecular Structure file(s) for 2VPY Structure Factors (1235 Kb) Retrieve 2VPY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VPY from S2C, [Save to disk] Re-refined 2vpy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VPY 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 2VPY

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 2VPY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vpy_A] [2vpy_F] [2vpy_B] [2vpy_G] [2vpy_E] [2vpy] [2vpy_C] SWISS-PROT database: [Q72LA4] [Q72LA5] [Q72LA6] Domain organization of [Q72LA4_THET2] [Q72LA5_THET2] [Q72LA6_THET2] by SWISSPFAM Domain found in 2VPY: [Molybdop_Fe4S4 ] by SMART

Other resources with information on 2VPY

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

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