3s39 Summary

pdbe.org/3s39
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Structure of Thermus thermophilus cytochrome ba3 oxidase 60s after Xe depressurization

The structure was published by Luna, V.M., Fee, J.A., Deniz, A.A., and Stout, C.D., in 2012 in a paper entitled "Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 4.8 Å and deposited in 2011.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 2, and Cytochrome c oxidase polypeptide 2A.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotrimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A Cytochrome c oxidase subunit 1 Q5SJ79 (2-562) (COX1_THET8)search Thermus thermophilus HB8search 100% 568 98%
B Cytochrome c oxidase subunit 2 Q5SJ80 (3-168) (COX2_THET8)search Thermus thermophilus HB8search 99% 166 100%
C Cytochrome c oxidase polypeptide 2A P82543 (2-34) (COXA_THET8)search Thermus thermophilus HB8search 97% 33 100%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
Q5SJ79 (2 - 562) Cytochrome c oxidase subunit 1 Thermus thermophilus HB8
Q5SJ80 (3 - 168) Cytochrome c oxidase subunit 2 Thermus thermophilus HB8
P82543 (2 - 34) Cytochrome c oxidase polypeptide 2A Thermus thermophilus HB8

Chain Sequence family (Pfam)
A (Q5SJ79) PF00115: Cytochrome C and Quinol oxidase polypeptide Isearch
B (Q5SJ80) PF00116: Cytochrome C oxidase subunit II, periplasmic domainsearch, PF09125: Cytochrome C oxidase subunit II, transmembranesearch
C (P82543) PF08113: Cytochrome c oxidase subunit IIa familysearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A (Q5SJ79) cytochrome-c oxidase activitysearch electron carrier activitysearch heme bindingsearch iron ion bindingsearch oxidoreductase activitysearch metal ion bindingsearch hydrogen ion transmembrane transportsearch oxidation-reduction processsearch ion transportsearch oxidative phosphorylationsearch aerobic respirationsearch proton transportsearch respiratory chainsearch integral component of membranesearch membranesearch plasma membranesearch
B (Q5SJ80) cytochrome-c oxidase activitysearch copper ion bindingsearch metal ion bindingsearch oxidoreductase activitysearch electron transport chainsearch hydrogen ion transmembrane transportsearch oxidation-reduction processsearch integral component of membranesearch membranesearch plasma membranesearch respiratory chainsearch
C (P82543) cytochrome-c oxidase activitysearch oxidoreductase activitysearch ion transportsearch proton transportsearch hydrogen ion transmembrane transportsearch oxidation-reduction processsearch plasma membranesearch integral component of membranesearch membranesearch respiratory chainsearch

Chain InterPro annotation
A Cytochrome c oxidase subunit Isearch Cytochrome c oxidase, subunit I, copper-binding sitesearch Cytochrome c oxidase, subunit I domainsearch
B Copper centre Cu(A)search Cytochrome c oxidase subunit II C-terminalsearch Cupredoxinsearch Cytochrome C oxidase subunit II, transmembrane domainsearch Cytochrome C oxidase subunit IIa, transmembrane domainsearch GPCR, rhodopsin-like, 7TMsearch
C Cytochrome c oxidase polypeptide 2Asearch