3AG3	Oxidoreductase	date	Mar 19, 2010
title	Bovine Heart Cytochrome C Oxidase In The Nitric Oxide-Bound Reduced State At 100 K
authors	K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabe E.Yamashita, T.Tsukihara, S.Yoshikawa
compound		source
Molecule: Cytochrome C Oxidase Subunit 1 Chain: A, N Synonym: Cytochrome C Oxidase Polypeptide I Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 2 Chain: B, O Synonym: Cytochrome C Oxidase Polypeptide II Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 3 Chain: C, P Synonym: Cytochrome C Oxidase Polypeptide III Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 4 Isoform 1 Chain: D, Q Synonym: Cytochrome C Oxidase Subunit Iv Isoform 1, Cox Iv- Cytochrome C Oxidase Polypeptide Iv; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 5a Chain: E, R Synonym: Cytochrome C Oxidase Polypeptide Va Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 5b Chain: F, S Synonym: Cytochrome C Oxidase Polypeptide Vb, Cytochrome C Polypeptide Via; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 6a2 Chain: G, T Synonym: Cytochrome C Oxidase Polypeptide Via-Heart, Coxvia Cytochrome C Oxidase Polypeptide Vib; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 6b1 Chain: H, U Synonym: Cytochrome C Oxidase Subunit Vib Isoform 1, Cox Vi Cytochrome C Oxidase Polypeptide Vii, Cytochrome C Oxidase Aed; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 6c Chain: I, V Synonym: Cytochrome C Oxidase Polypeptide Vic, Cytochrome C Subunit Sta; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Polypeptide 7a1 Chain: J, W Synonym: Cytochrome C Oxidase Polypeptide Viia-Heart, Cytoc Oxidase Subunit Viia-H, Cox Viia-M, Viiic; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 7b Chain: K, X Synonym: Cytochrome C Oxidase Polypeptide Viib, Ihq Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 7c Chain: L, Y Synonym: Cytochrome C Oxidase Polypeptide Viic, Cytochrome Polypeptide Viiia; Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
Molecule: Cytochrome C Oxidase Subunit 8b Chain: M, Z Synonym: Cytochrome C Oxidase Subunit 8h, Cytochrome C Oxid Polypeptide Viii-Heart, Cytochrome C Oxidase Subunit 8-1, V Ec: 1.9.3.1		Organism_scientific: Bos Taurus Organism_common: Bovine Organism_taxid: 9913
symmetry	Space Group: P 21 21 21	R_factor 0.175 R_Free 0.203
crystal cell	length a length b length c angle alpha angle beta angle gamma 182.289 208.358 177.916 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.80 Å
ligand	CDL, CHD, CU, CUA, DMU, FME, HEA, MG, NA, NO, PEK, PGV, PSC, SAC, TGL, TPO, UNX, ZN	enzyme	Oxidoreductase E.C.1.9.3.1 BRENDA
note	3AG3 is a representative structure
Gene Ontology	Chain Function Process Component C, P cytochrome-c oxidase activit... heme-copper terminal oxidase... aerobic electron transport c... respiratory electron transpo... mitochondrion mitochondrial inner membrane... membrane integral to membrane E, R cytochrome-c oxidase activit... metal ion binding mitochondrion mitochondrial inner membrane... membrane H, U cytochrome-c oxidase activit... mitochondrion mitochondrial inner membrane... mitochondrial intermembrane ... J, W cytochrome-c oxidase activit... electron carrier activity mitochondrion mitochondrial inner membrane... mitochondrial respiratory ch... membrane integral to membrane K, X cytochrome-c oxidase activit... central nervous system devel... mitochondrion mitochondrial inner membrane... mitochondrial respiratory ch... membrane integral to membrane N, A cytochrome-c oxidase activit... iron ion binding electron carrier activity oxidoreductase activity heme binding metal ion binding oxidative phosphorylation aerobic respiration electron transport chain oxidation-reduction process mitochondrion mitochondrial inner membrane... membrane integral to membrane respiratory chain O, B cytochrome-c oxidase activit... copper ion binding oxidoreductase activity metal ion binding electron transport chain mitochondrion mitochondrial inner membrane... membrane integral to membrane respiratory chain Q, D cytochrome-c oxidase activit... nucleus mitochondrion mitochondrial inner membrane... mitochondrial respiratory ch... membrane integral to membrane S, F cytochrome-c oxidase activit... metal ion binding mitochondrion mitochondrial envelope mitochondrial inner membrane... membrane T, G cytochrome-c oxidase activit... mitochondrion mitochondrial inner membrane... mitochondrial respiratory ch... membrane integral to membrane Y, V, Z, M, L, I cytochrome-c oxidase activit... mitochondrion mitochondrial inner membrane... membrane integral to membrane
Primary reference	Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate., Muramoto K, Ohta K, Shinzawa-Itoh K, Kanda K, Taniguchi M, Nabekura H, Yamashita E, Tsukihara T, Yoshikawa S, Proc Natl Acad Sci U S A. 2010 Apr 12. PMID:20385840

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (686 Kb) [Save to disk] Biological Unit Coordinates (3ag3.pdb1.gz) 337 Kb Biological Unit Coordinates (3ag3.pdb2.gz) 336 Kb LPC: Ligand-Protein Contacts for 3AG3 CSU: Contacts of Structural Units for 3AG3 Structure Factors (4740 Kb) Retrieve 3AG3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3AG3 from S2C, [Save to disk] Re-refined 3ag3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3AG3 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3AG3

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 3AG3, from MSDmotif at EBI Fold representative 3ag3 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ag3_A] [3ag3_B] [3ag3_C] [3ag3_D] [3ag3_E] [3ag3_F] [3ag3_G] [3ag3_H] [3ag3_I] [3ag3_J] [3ag3_K] [3ag3_L] [3ag3_M] [3ag3_N] [3ag3_O] [3ag3_P] [3ag3_Q] [3ag3_R] [3ag3_S] [3ag3_T] [3ag3_U] [3ag3_V] [3ag3_W] [3ag3_X] [3ag3_Y] [3ag3_Z] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3AG3 with the sequences similar proteins can be viewed for 3AG3's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.

Other resources with information on 3AG3

Community annotation for 3AG3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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