3EHB	Oxidoreductase Immune System	date	Sep 12, 2008
title	A D-Pathway Mutation Decouples The Paracoccus Denitrificans C Oxidase By Altering The Side Chain Orientation Of A Dista Conserved Glutamate
authors	J.Koepke, H.Mueller, G.Peng
compound		source
Molecule: Cytochrome C Oxidase Subunit 1-Beta Chain: A Fragment: Unp Residues 17-545 Synonym: Cytochrome C Oxidase Polypeptide I-Beta, Cytochrom Subunit 1-Beta; Ec: 1.9.3.1 Engineered: Yes Mutation: Yes		Organism_scientific: Paracoccus Denitrificans Organism_taxid: 266 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Cytochrome C Oxidase Subunit 2 Chain: B Synonym: Cytochrome C Oxidase Polypeptide II, Cytochrome Aa 2, Oxidase Aa(3) Subunit 2; Ec: 1.9.3.1 Engineered: Yes		Organism_scientific: Paracoccus Denitrificans Organism_taxid: 266 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Fv Fragment Chain H Chain: C Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Fv Fragment Chain L Chain: D Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: Mouse Organism_taxid: 10090 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.205 R_Free 0.242
crystal cell	length a length b length c angle alpha angle beta angle gamma 84.461 151.332 157.487 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.32 Å
ligand	CA, CU, HEA, LDA, LMT, MG, PER	enzyme	Oxidoreductase E.C.1.9.3.1 BRENDA
Gene Ontology	Chain Function Process Component A cytochrome-c oxidase activit... B C
Primary reference	A D-pathway mutation decouples the paracoccusdenitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate., Durr KL, Koepke J, Hellwig P, Muller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H, J Mol Biol. 2008 Dec 26;384(4):865-77. Epub 2008 Oct 9. PMID:18930738

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (194 Kb) [Save to disk] Biological Unit Coordinates (3ehb.pdb1.gz) 181 Kb LPC: Ligand-Protein Contacts for 3EHB CSU: Contacts of Structural Units for 3EHB Likely Quarternary Molecular Structure file(s) for 3EHB Structure Factors (1509 Kb) Retrieve 3EHB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3EHB from S2C, [Save to disk] Re-refined 3ehb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3EHB 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 3EHB

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 3EHB, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ehb_D] [3ehb] [3ehb_B] [3ehb_C] [3ehb_A] SWISS-PROT database: [P98002] [P08306] [P18525] Belongs to the proton-translocating cytochrome oxidase (cox) superfamily according to TCDB. Domain organization of [COX1B_PARDE] [COX2_PARDE] [HVM54_MOUSE] by SWISSPFAM Domain found in 3EHB: [IGv ] by SMART

Other resources with information on 3EHB

Community annotation for 3EHB at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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