1Y5N	Oxidoreductase	date	Dec 02, 2004
title	The Crystal Structure Of The Narghi Mutant Nari-K86a In Comp Pentachlorophenol
authors	M.G.Bertero, R.A.Rothery, N.Boroumand, M.Palak, F.Blasco, N.Ginet J.H.Weiner, N.C.J.Strynadka
compound		source
Molecule: Respiratory Nitrate Reductase 1 Alpha Chain Chain: A Synonym: Narg, Nitrate Reductase A Alpha Subunit, Quinol-Ni Oxidoreductase Alpha Subunit; Ec: 1.7.99.4 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Narg Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Lcb79 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pva700
Molecule: Respiratory Nitrate Reductase 1 Beta Chain Chain: B Synonym: Narh, Nitrate Reductase A Beta Subunit, Quinol-Nit Oxidoreductase Beta Subunit; Ec: 1.7.99.4 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Narh Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Lcb79 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pva700
Molecule: Respiratory Nitrate Reductase 1 Gamma Chain Chain: C Synonym: Nari, Nitrate Reductase A Gamma Subunit, Quinol-Ni Oxidoreductase Gamma Subunit, Cytochrome B-Nr; Ec: 1.7.99.4 Engineered: Yes Mutation: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Nari Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Lcb79 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pva700
symmetry	Space Group: C 2 2 21	R_factor 0.190 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 154.258 241.957 140.121 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	3PH, 6MO, AGA, F3S, FME, HEM, MD1, PCI, SF4	enzyme	Oxidoreductase E.C.1.7.99.4 BRENDA
related structures	by homologous chain: 1Y5L
Gene Ontology	Chain Function Process Component A electron transfer activity B electron transfer activity C
Primary reference	Structural and biochemical characterization of a quinol binding site of escherichia coli nitrate reductase A (NarGHI)., Bertero MG, Rothery RR, Boroumand N, Palak M, Blasco F, Ginet N, Weiner JH, Strynadka NC, J Biol Chem 2004 Dec 22;. PMID:15615728

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (329 Kb) [Save to disk] Biological Unit Coordinates (1y5n.pdb1.gz) 320 Kb Biological Unit Coordinates (1y5n.pdb2.gz) 631 Kb LPC: Ligand-Protein Contacts for 1Y5N CSU: Contacts of Structural Units for 1Y5N Likely Quarternary Molecular Structure file(s) for 1Y5N Structure Factors (660 Kb) Retrieve 1Y5N in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1Y5N from S2C, [Save to disk] Re-refined 1y5n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1Y5N 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 1Y5N

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 1Y5N, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1y5n] [1y5n_C] [1y5n_A] [1y5n_B] SWISS-PROT database: [P09152] [P11349] [P11350] Belongs to the prokaryotic molybdopterin-containing oxidoreductase (pmo) family according to TCDB. Domain organization of [NARG_ECOLI] [NARH_ECOLI] [NARI_ECOLI] by SWISSPFAM Domain found in 1Y5N: [Molybdop_Fe4S4 ] by SMART

Other resources with information on 1Y5N

Community annotation for 1Y5N at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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