1Y7MA

Crystal structure of the b. subtilis ykud protein at 2 a resolution
Total Genus 38
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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
38
sequence length
164
structure length
164
Chain Sequence
MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR
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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 Structural genomics, unknown function
molecule keywords hypothetical protein BSU14040
publication title B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.
pubmed doi rcsb
source organism Bacillus subtilis subsp. subtilis str. 168
total genus 38
structure length 164
sequence length 164
chains with identical sequence B
ec nomenclature
pdb deposition date 2004-12-09

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01476 LysM LysM domain
A PF03734 YkuD L,D-transpeptidase catalytic domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.440.10 Mainly Beta Beta Barrel L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like 1y7mA02
3.10.350.10 Alpha Beta Roll Membrane-bound Lytic Murein Transglycosylase D; Chain A LysM domain 1y7mA01
5DUJA 2HKLA 4A1KA 2MKXA 3U1QA 4JMNA 1E0GA 5DZPA 5DC2A 4LPQA 3VYPA 5BUMA 4LZHA 1ZATA 4B8VA 3VAEA 4A52A 5D7HA 4HUCA 3ZQDA 5E51A 5E1IA 4GSRA 4QR7A 5DZJA 4QTFA 5DU7A 4A1JA 5E5LA 3TURA 2MTZA 5E1GA 5C8OA 1Y7MA 3TX4A 3ZGPA 4Z7AA 2L9YA 4K73A 4QRAA 4JMXA 3VYOA 5K69A 3VYNA 5DVPA 3U1PA 3ZG4A 2DJPA 5DCCA 2LTFA 5K2LA 5C8QB 4A1IA 5C8PA 4QRBA 4ZFQA 4PXVA 5LBGA 4GSQA 4B9HA 5LB1A 4XVOA 4GSUA
chains in the Genus database with same CATH superfamily
5DUJA 2HKLA 4A1KA 2MKXA 3U1QA 4JMNA 1E0GA 5DZPA 5DC2A 4LPQA 3VYPA 5BUMA 4LZHA 1ZATA 4B8VA 3VAEA 4A52A 5D7HA 4HUCA 3ZQDA 5E51A 5E1IA 4GSRA 4QR7A 5DZJA 4QTFA 5DU7A 4A1JA 5E5LA 3TURA 2MTZA 5E1GA 5C8OA 1Y7MA 3TX4A 3ZGPA 4Z7AA 2L9YA 4K73A 4QRAA 4JMXA 3VYOA 5K69A 3VYNA 5DVPA 3U1PA 3ZG4A 2DJPA 5DCCA 2LTFA 5K2LA 5C8QB 4A1IA 5C8PA 4QRBA 4ZFQA 4PXVA 5LBGA 4GSQA 4B9HA 5LB1A 4XVOA 4GSUA
chains in the Genus database with same CATH topology
5DUJA 2HKLA 4A1KA 2MKXA 3U1QA 4JMNA 1E0GA 5DZPA 5DC2A 4LPQA 3VYPA 5BUMA 4LZHA 1ZATA 4B8VA 3VAEA 4A52A 5D7HA 4HUCA 3ZQDA 5E51A 5E1IA 4GSRA 4QR7A 5DZJA 4QTFA 5DU7A 4A1JA 5E5LA 3TURA 2MTZA 5E1GA 5C8OA 1Y7MA 3TX4A 3ZGPA 4Z7AA 2L9YA 4K73A 4QRAA 4JMXA 3VYOA 5K69A 3VYNA 5DVPA 3U1PA 3ZG4A 2DJPA 5DCCA 2LTFA 5K2LA 5C8QB 4A1IA 5C8PA 4QRBA 4ZFQA 4PXVA 5LBGA 4GSQA 4B9HA 5LB1A 4XVOA 4GSUA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5DUJ A;  2HKL A;  4A1K A;  2MKX A;  3U1Q A;  4JMN A;  1E0G A;  5DZP A;  5DC2 A;  4LPQ A;  3VYP A;  5BUM A;  4LZH A;  1ZAT A;  4B8V A;  3VAE A;  4A52 A;  5D7H A;  4HUC A;  3ZQD A;  5E51 A;  5E1I A;  4GSR A;  4QR7 A;  5DZJ A;  4QTF A;  5DU7 A;  4A1J A;  5E5L A;  3TUR A;  2MTZ A;  5E1G A;  5C8O A;  1Y7M A;  3TX4 A;  3ZGP A;  4Z7A A;  2L9Y A;  4K73 A;  4QRA A;  4JMX A;  3VYO A;  5K69 A;  3VYN A;  5DVP A;  3U1P A;  3ZG4 A;  2DJP A;  5DCC A;  2LTF A;  5K2L A;  5C8Q B;  4A1I A;  5C8P A;  4QRB A;  4ZFQ A;  4PXV A;  5LBG A;  4GSQ A;  4B9H A;  5LB1 A;  4XVO A;  4GSU A; 
#chains in the Genus database with same CATH topology
 5DUJ A;  2HKL A;  4A1K A;  2MKX A;  3U1Q A;  4JMN A;  1E0G A;  5DZP A;  5DC2 A;  4LPQ A;  3VYP A;  5BUM A;  4LZH A;  1ZAT A;  4B8V A;  3VAE A;  4A52 A;  5D7H A;  4HUC A;  3ZQD A;  5E51 A;  5E1I A;  4GSR A;  4QR7 A;  5DZJ A;  4QTF A;  5DU7 A;  4A1J A;  5E5L A;  3TUR A;  2MTZ A;  5E1G A;  5C8O A;  1Y7M A;  3TX4 A;  3ZGP A;  4Z7A A;  2L9Y A;  4K73 A;  4QRA A;  4JMX A;  3VYO A;  5K69 A;  3VYN A;  5DVP A;  3U1P A;  3ZG4 A;  2DJP A;  5DCC A;  2LTF A;  5K2L A;  5C8Q B;  4A1I A;  5C8P A;  4QRB A;  4ZFQ A;  4PXV A;  5LBG A;  4GSQ A;  4B9H A;  5LB1 A;  4XVO A;  4GSU A; 
#chains in the Genus database with same CATH homology
 5DUJ A;  2HKL A;  4A1K A;  2MKX A;  3U1Q A;  4JMN A;  1E0G A;  5DZP A;  5DC2 A;  4LPQ A;  3VYP A;  5BUM A;  4LZH A;  1ZAT A;  4B8V A;  3VAE A;  4A52 A;  5D7H A;  4HUC A;  3ZQD A;  5E51 A;  5E1I A;  4GSR A;  4QR7 A;  5DZJ A;  4QTF A;  5DU7 A;  4A1J A;  5E5L A;  3TUR A;  2MTZ A;  5E1G A;  5C8O A;  1Y7M A;  3TX4 A;  3ZGP A;  4Z7A A;  2L9Y A;  4K73 A;  4QRA A;  4JMX A;  3VYO A;  5K69 A;  3VYN A;  5DVP A;  3U1P A;  3ZG4 A;  2DJP A;  5DCC A;  2LTF A;  5K2L A;  5C8Q B;  4A1I A;  5C8P A;  4QRB A;  4ZFQ A;  4PXV A;  5LBG A;  4GSQ A;  4B9H A;  5LB1 A;  4XVO A;  4GSU 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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