2QPDA

An unexpected outcome of surface-engineering an integral membrane protein: improved crystallization of cytochrome ba3 oxidase from thermus thermophilus
Total Genus 205
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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
205
sequence length
557
structure length
557
Chain Sequence
SEISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGRLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW
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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 Cytochrome c oxidase subunit 1
publication title An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
pubmed doi rcsb
source organism Thermus thermophilus
total genus 205
structure length 557
sequence length 557
ec nomenclature ec 1.9.3.1: Cytochrome-c oxidase.
pdb deposition date 2007-07-23

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 2qpdA00
4XYDA 3O0RB 3OM3A 1OCZA 3MK7A 3WG7A 3ABMA 1M57A 2ZXWA 2EIKA 4G7QA 1FFTA 3WFEB 3S3DA 2EIMA 3ASOA 3AYFA 3EH4A 4FAAA 1V54A 1QLEA 3AG2A 3FYEA 1OCCA 3HB3A 3QJSA 4G7SA 3EHBA 2DYRA 3QJRA 3AG1A 3ABKA 3FYIA 3QJQA 3OMNA 2Y69A 3AG3A 4N4YA 3AYGA 2OCCA 5B1AA 3WFBB 2GSMA 4G71A 1AR1A 4FA7A 4G72A 3ABLA 2QPEA 3BVDA 3S8FA 5IY5A 3AG4A 4G7RA 3OMAA 3QJUA 3WFDB 5B1BA 4GP5A 3EH5A 4GP8A 2YEVA 2EILA 3QJTA 2EINA 3S3BA 3EH3A 1XMEA 3DTUA 1EHKA 4GP4A 3X2QA 5B3SA 2QPDA 3OMIA 1M56A 3WFCB 1V55A 4G70A 5DJQA 1OCRA 3S3CA 1OCOA 2DYSA 3S8GA 3QJVA 3ASNA 2EIJA
chains in the Genus database with same CATH superfamily
4XYDA 3O0RB 3OM3A 1OCZA 3MK7A 3WG7A 3ABMA 1M57A 2ZXWA 2EIKA 4G7QA 1FFTA 3WFEB 3S3DA 2EIMA 3ASOA 3AYFA 3EH4A 4FAAA 1V54A 1QLEA 3AG2A 3FYEA 1OCCA 3HB3A 3QJSA 4G7SA 3EHBA 2DYRA 3QJRA 3AG1A 3ABKA 3FYIA 3QJQA 3OMNA 2Y69A 3AG3A 4N4YA 3AYGA 2OCCA 5B1AA 3WFBB 2GSMA 4G71A 1AR1A 4FA7A 4G72A 3ABLA 2QPEA 3BVDA 3S8FA 5IY5A 3AG4A 4G7RA 3OMAA 3QJUA 3WFDB 5B1BA 4GP5A 3EH5A 4GP8A 2YEVA 2EILA 3QJTA 2EINA 3S3BA 3EH3A 1XMEA 3DTUA 1EHKA 4GP4A 3X2QA 5B3SA 2QPDA 3OMIA 1M56A 3WFCB 1V55A 4G70A 5DJQA 1OCRA 3S3CA 1OCOA 2DYSA 3S8GA 3QJVA 3ASNA 2EIJA
chains in the Genus database with same CATH topology
4XYDA 3O0RB 3OM3A 1OCZA 3MK7A 3WG7A 3ABMA 1M57A 2ZXWA 2EIKA 4G7QA 1FFTA 3WFEB 3S3DA 2EIMA 3ASOA 3AYFA 3EH4A 4FAAA 1V54A 1QLEA 3AG2A 3FYEA 1OCCA 3HB3A 3QJSA 4G7SA 3EHBA 2DYRA 3QJRA 3AG1A 3ABKA 3FYIA 3QJQA 3OMNA 2Y69A 3AG3A 4N4YA 3AYGA 2OCCA 5B1AA 3WFBB 2GSMA 4G71A 1AR1A 4FA7A 4G72A 3ABLA 2QPEA 3BVDA 3S8FA 5IY5A 3AG4A 4G7RA 3OMAA 3QJUA 3WFDB 5B1BA 4GP5A 3EH5A 4GP8A 2YEVA 2EILA 3QJTA 2EINA 3S3BA 3EH3A 1XMEA 3DTUA 1EHKA 4GP4A 3X2QA 5B3SA 2QPDA 3OMIA 1M56A 3WFCB 1V55A 4G70A 5DJQA 1OCRA 3S3CA 1OCOA 2DYSA 3S8GA 3QJVA 3ASNA 2EIJA
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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