1DY7	Oxidoreductase	date	Jan 28, 2000
title	Cytochrome Cd1 Nitrite Reductase, Co Complex
authors	T.Sjogren, M.Svensson-Ek, J.Hajdu, P.Brzezinski
compound		source
Molecule: Nitrite Reductase Chain: A, B Synonym: Cytochrome Cd1, Cytochrome Oxidase, Hydroxylamine Ec: 1.7.2.1, 1.7.99.1		Organism_scientific: Paracoccus Pantotrophus Organism_taxid: 82367 Cellular_location: Periplasm Other_details: Organism Formerly Known As Thiosphaera Panto
symmetry	Space Group: P 1 21 1	R_factor 0.178 R_Free 0.199
crystal cell	length a length b length c angle alpha angle beta angle gamma 106.940 61.040 100.390 90.00 111.77 90.00
method	X-Ray Diffraction	resolution	1.60 Å
ligand	CMO, DHE, GOL, HEC, SO4	enzyme	Oxidoreductase E.C.1.7.2.1 BRENDA
related structures	by homologous chain: 1E2R, 1HJ3
Gene Ontology	Chain Function Process Component A, B electron transfer activity
Primary reference	Proton-coupled structural changes upon binding of carbon monoxide to cytochrome cd1: a combined flash photolysis and X-ray crystallography study., Sjogren T, Svensson-Ek M, Hajdu J, Brzezinski P, Biochemistry 2000 Sep 12;39(36):10967-74. PMID:10998233

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (181 Kb) [Save to disk] Biological Unit Coordinates (1dy7.pdb1.gz) 173 Kb LPC: Ligand-Protein Contacts for 1DY7 CSU: Contacts of Structural Units for 1DY7 Likely Quarternary Molecular Structure file(s) for 1DY7 Structure Factors (1052 Kb) Retrieve 1DY7 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1DY7 from S2C, [Save to disk] Re-refined 1dy7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1DY7 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 1DY7

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 1DY7, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1dy7a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1dy7b2, region B:136-567 [Jmol] [rasmolscript] [script source]     - Domain d1dy7b1, region B:32-135 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1dy7] [1dy7_A] [1dy7_B] SWISS-PROT database: [P72181] Domain organization of [NIRS_PARPN] by SWISSPFAM

Other resources with information on 1DY7

Community annotation for 1DY7 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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