5DJQA

The structure of cbb3 cytochrome oxidase.
Total Genus 196
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
196
sequence length
466
structure length
466
Chain Sequence
TSTAYSYKVVRQFAIMTVVWGIVGMGLGVFIAAQLAWPFLNFDLPWTSFGRLRPLHTNAVIFAFGGCALFATSYYSVQRTCQTTLFAPKLAAFTFWGWQLVILLAAISLPLGFTSSKEYAELEWPIDILITIVWVAYAVVFFGTLAKRKVKHIYVGNWFFGAFILTVAILHVVNNLEIPVTAMKSYSLYAGATDAMVQWWYGHNAVGFFLTAGFLGIMYYFVPKQAERPVYSYRLSIVHFWALITVYIWAGPHHLHYTALPDWAQSLGMVMSLILLAPSWGGMINGMMTLSGAWHKLRSDPILRFLVVSLAFYGMSTFEGPMMAIKTVNALSHYTDWTIGHVHAGALGWVAMVSIGALYHLVPKVFGREQMHSIGLINTHFWLATIGTVLYIASMWVNGIAQGLMWRAINDDGTLTYSFVESLEASHPGFVVRMIGGAIFFAGMLVMAYNTWRTVQAAKPAEYDAA
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Oxidoreductase
molecule keywords Cbb3-type cytochrome c oxidase subunit CcoN1
publication title The structure of cbb3 cytochrome oxidase provides insights into proton pumping.
pubmed doi rcsb
total genus 196
structure length 466
sequence length 466
chains with identical sequence D, G, K
ec nomenclature ec 1.9.3.1: Cytochrome-c oxidase.
pdb deposition date 2015-09-02

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00115 COX1 Cytochrome C and Quinol oxidase polypeptide I
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.20.210.10 Mainly Alpha Up-down Bundle Cytochrome C Oxidase; Chain A Cytochrome c oxidase-like, subunit I domain 5djqA00
3S8FA 2EINA 3AG1A 3QJRA 3HB3A 1XMEA 4G71A 4G7SA 3WFEB 5B3SA 2ZXWA 4G70A 3ABLA 3EH4A 3WG7A 4GP8A 4G72A 3ASNA 3EHBA 4FA7A 4GP5A 4FAAA 1OCZA 2EIJA 3OMNA 2Y69A 1QLEA 2YEVA 1V55A 3DTUA 3ABMA 3EH5A 5B1BA 4N4YA 3WFCB 1FFTA 3OMIA 3S8GA 2QPEA 3ABKA 3OMAA 2OCCA 2DYSA 3OM3A 5DJQA 3S3DA 3S3BA 2EIKA 4G7RA 2EILA 3QJUA 2DYRA 3AYGA 1M57A 3X2QA 2GSMA 3AG4A 2EIMA 1OCRA 1V54A 3WFBB 1EHKA 5IY5A 3FYEA 5B1AA 3EH3A 3WFDB 3QJTA 4XYDA 3S3CA 3ASOA 3O0RB 3AYFA 2QPDA 4GP4A 3BVDA 3QJQA 4G7QA 3QJVA 1AR1A 1OCOA 1OCCA 3QJSA 3AG3A 3AG2A 3MK7A 3FYIA 1M56A
chains in the Genus database with same CATH superfamily
3S8FA 2EINA 3AG1A 3QJRA 3HB3A 1XMEA 4G71A 4G7SA 3WFEB 5B3SA 2ZXWA 4G70A 3ABLA 3EH4A 3WG7A 4GP8A 4G72A 3ASNA 3EHBA 4FA7A 4GP5A 4FAAA 1OCZA 2EIJA 3OMNA 2Y69A 1QLEA 2YEVA 1V55A 3DTUA 3ABMA 3EH5A 5B1BA 4N4YA 3WFCB 1FFTA 3OMIA 3S8GA 2QPEA 3ABKA 3OMAA 2OCCA 2DYSA 3OM3A 5DJQA 3S3DA 3S3BA 2EIKA 4G7RA 2EILA 3QJUA 2DYRA 3AYGA 1M57A 3X2QA 2GSMA 3AG4A 2EIMA 1OCRA 1V54A 3WFBB 1EHKA 5IY5A 3FYEA 5B1AA 3EH3A 3WFDB 3QJTA 4XYDA 3S3CA 3ASOA 3O0RB 3AYFA 2QPDA 4GP4A 3BVDA 3QJQA 4G7QA 3QJVA 1AR1A 1OCOA 1OCCA 3QJSA 3AG3A 3AG2A 3MK7A 3FYIA 1M56A
chains in the Genus database with same CATH topology
3S8FA 2EINA 3AG1A 3QJRA 3HB3A 1XMEA 4G71A 4G7SA 3WFEB 5B3SA 2ZXWA 4G70A 3ABLA 3EH4A 3WG7A 4GP8A 4G72A 3ASNA 3EHBA 4FA7A 4GP5A 4FAAA 1OCZA 2EIJA 3OMNA 2Y69A 1QLEA 2YEVA 1V55A 3DTUA 3ABMA 3EH5A 5B1BA 4N4YA 3WFCB 1FFTA 3OMIA 3S8GA 2QPEA 3ABKA 3OMAA 2OCCA 2DYSA 3OM3A 5DJQA 3S3DA 3S3BA 2EIKA 4G7RA 2EILA 3QJUA 2DYRA 3AYGA 1M57A 3X2QA 2GSMA 3AG4A 2EIMA 1OCRA 1V54A 3WFBB 1EHKA 5IY5A 3FYEA 5B1AA 3EH3A 3WFDB 3QJTA 4XYDA 3S3CA 3ASOA 3O0RB 3AYFA 2QPDA 4GP4A 3BVDA 3QJQA 4G7QA 3QJVA 1AR1A 1OCOA 1OCCA 3QJSA 3AG3A 3AG2A 3MK7A 3FYIA 1M56A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3S8F A;  2EIN A;  3AG1 A;  3QJR A;  3HB3 A;  1XME A;  4G71 A;  4G7S A;  3WFE B;  5B3S A;  2ZXW A;  4G70 A;  3ABL A;  3EH4 A;  3WG7 A;  4GP8 A;  4G72 A;  3ASN A;  3EHB A;  4FA7 A;  4GP5 A;  4FAA A;  1OCZ A;  2EIJ A;  3OMN A;  2Y69 A;  1QLE A;  2YEV A;  1V55 A;  3DTU A;  3ABM A;  3EH5 A;  5B1B A;  4N4Y A;  3WFC B;  1FFT A;  3OMI A;  3S8G A;  2QPE A;  3ABK A;  3OMA A;  2OCC A;  2DYS A;  3OM3 A;  5DJQ A;  3S3D A;  3S3B A;  2EIK A;  4G7R A;  2EIL A;  3QJU A;  2DYR A;  3AYG A;  1M57 A;  3X2Q A;  2GSM A;  3AG4 A;  2EIM A;  1OCR A;  1V54 A;  3WFB B;  1EHK A;  5IY5 A;  3FYE A;  5B1A A;  3EH3 A;  3WFD B;  3QJT A;  4XYD A;  3S3C A;  3ASO A;  3O0R B;  3AYF A;  2QPD A;  4GP4 A;  3BVD A;  3QJQ A;  4G7Q A;  3QJV A;  1AR1 A;  1OCO A;  1OCC A;  3QJS A;  3AG3 A;  3AG2 A;  3MK7 A;  3FYI A;  1M56 A; 
#chains in the Genus database with same CATH topology
 3S8F A;  2EIN A;  3AG1 A;  3QJR A;  3HB3 A;  1XME A;  4G71 A;  4G7S A;  3WFE B;  5B3S A;  2ZXW A;  4G70 A;  3ABL A;  3EH4 A;  3WG7 A;  4GP8 A;  4G72 A;  3ASN A;  3EHB A;  4FA7 A;  4GP5 A;  4FAA A;  1OCZ A;  2EIJ A;  3OMN A;  2Y69 A;  1QLE A;  2YEV A;  1V55 A;  3DTU A;  3ABM A;  3EH5 A;  5B1B A;  4N4Y A;  3WFC B;  1FFT A;  3OMI A;  3S8G A;  2QPE A;  3ABK A;  3OMA A;  2OCC A;  2DYS A;  3OM3 A;  5DJQ A;  3S3D A;  3S3B A;  2EIK A;  4G7R A;  2EIL A;  3QJU A;  2DYR A;  3AYG A;  1M57 A;  3X2Q A;  2GSM A;  3AG4 A;  2EIM A;  1OCR A;  1V54 A;  3WFB B;  1EHK A;  5IY5 A;  3FYE A;  5B1A A;  3EH3 A;  3WFD B;  3QJT A;  4XYD A;  3S3C A;  3ASO A;  3O0R B;  3AYF A;  2QPD A;  4GP4 A;  3BVD A;  3QJQ A;  4G7Q A;  3QJV A;  1AR1 A;  1OCO A;  1OCC A;  3QJS A;  3AG3 A;  3AG2 A;  3MK7 A;  3FYI A;  1M56 A; 
#chains in the Genus database with same CATH homology
 3S8F A;  2EIN A;  3AG1 A;  3QJR A;  3HB3 A;  1XME A;  4G71 A;  4G7S A;  3WFE B;  5B3S A;  2ZXW A;  4G70 A;  3ABL A;  3EH4 A;  3WG7 A;  4GP8 A;  4G72 A;  3ASN A;  3EHB A;  4FA7 A;  4GP5 A;  4FAA A;  1OCZ A;  2EIJ A;  3OMN A;  2Y69 A;  1QLE A;  2YEV A;  1V55 A;  3DTU A;  3ABM A;  3EH5 A;  5B1B A;  4N4Y A;  3WFC B;  1FFT A;  3OMI A;  3S8G A;  2QPE A;  3ABK A;  3OMA A;  2OCC A;  2DYS A;  3OM3 A;  5DJQ A;  3S3D A;  3S3B A;  2EIK A;  4G7R A;  2EIL A;  3QJU A;  2DYR A;  3AYG A;  1M57 A;  3X2Q A;  2GSM A;  3AG4 A;  2EIM A;  1OCR A;  1V54 A;  3WFB B;  1EHK A;  5IY5 A;  3FYE A;  5B1A A;  3EH3 A;  3WFD B;  3QJT A;  4XYD A;  3S3C A;  3ASO A;  3O0R B;  3AYF A;  2QPD A;  4GP4 A;  3BVD A;  3QJQ A;  4G7Q A;  3QJV A;  1AR1 A;  1OCO A;  1OCC A;  3QJS A;  3AG3 A;  3AG2 A;  3MK7 A;  3FYI A;  1M56 A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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