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 |
45
|
sequence length |
165
|
structure length |
165
|
Chain Sequence |
GMLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSAAHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR
|
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.
After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.
| publication title |
Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase from B. Subtilis.
rcsb |
| molecule tags |
Transferase
|
| source organism |
Bacillus subtilis
|
| molecule keywords |
PUTATIVE L, D-TRANSPEPTIDASE YKUD
|
| total genus |
45
|
| structure length |
165
|
| sequence length |
165
|
| chains with identical sequence |
B, C, D, E, F, G, H
|
| ec nomenclature |
ec
2.-.-.-: |
| pdb deposition date | 2011-09-15 |
| 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
| Class | Architecture | Topology | Homology | Domain |
|---|---|---|---|---|---|
| Mainly Beta | Beta Barrel | L,D-transpeptidase catalytic domain-like | L,D-transpeptidase catalytic domain-like | ||
| Alpha Beta | Roll | Membrane-bound Lytic Murein Transglycosylase D; Chain A | LysM domain |
#chains in the Genus database with same CATH superfamily 4B9H A; 1Y7M A; 5C8O A; 5DU7 A; 4QTF A; 2DJP A; 5E1I A; 5C8Q B; 3VAE A; 3TUR A; 4HUC A; 5E5L A; 4JMX A; 4ZFQ A; 4A52 A; 5LB1 A; 4K73 A; 2MKX A; 3TX4 A; 5C8P A; 3U1P A; 4QR7 A; 4Z7A A; 3ZQD A; 3ZG4 A; 5DC2 A; 5E51 A; 2L9Y A; 4LZH A; 5K2L A; 3U1Q A; 3ZGP A; 3VYN A; 5DUJ A; 5DCC A; 5DZP A; 4GSQ A; 4LPQ A; 5BUM A; 4JMN A; 2MTZ A; 3VYP A; 4QRB A; 1ZAT A; 3VYO A; 4QRA A; 2HKL A; 5LBG A; 4B8V A; 5DZJ A; 4XVO A; 4A1I A; 5K69 A; 4GSR A; 4A1K A; 5D7H A; 2LTF A; 4GSU A; 5E1G A; 4PXV A; 4A1J A; 1E0G A; 5DVP A; #chains in the Genus database with same CATH topology 4B9H A; 1Y7M A; 5C8O A; 5DU7 A; 4QTF A; 2DJP A; 5E1I A; 5C8Q B; 3VAE A; 3TUR A; 4HUC A; 5E5L A; 4JMX A; 4ZFQ A; 4A52 A; 5LB1 A; 4K73 A; 2MKX A; 3TX4 A; 5C8P A; 3U1P A; 4QR7 A; 4Z7A A; 3ZQD A; 3ZG4 A; 5DC2 A; 5E51 A; 2L9Y A; 4LZH A; 5K2L A; 3U1Q A; 3ZGP A; 3VYN A; 5DUJ A; 5DCC A; 5DZP A; 4GSQ A; 4LPQ A; 5BUM A; 4JMN A; 2MTZ A; 3VYP A; 4QRB A; 1ZAT A; 3VYO A; 4QRA A; 2HKL A; 5LBG A; 4B8V A; 5DZJ A; 4XVO A; 4A1I A; 5K69 A; 4GSR A; 4A1K A; 5D7H A; 2LTF A; 4GSU A; 5E1G A; 4PXV A; 4A1J A; 1E0G A; 5DVP A; #chains in the Genus database with same CATH homology 4B9H A; 1Y7M A; 5C8O A; 5DU7 A; 4QTF A; 2DJP A; 5E1I A; 5C8Q B; 3VAE A; 3TUR A; 4HUC A; 5E5L A; 4JMX A; 4ZFQ A; 4A52 A; 5LB1 A; 4K73 A; 2MKX A; 3TX4 A; 5C8P A; 3U1P A; 4QR7 A; 4Z7A A; 3ZQD A; 3ZG4 A; 5DC2 A; 5E51 A; 2L9Y A; 4LZH A; 5K2L A; 3U1Q A; 3ZGP A; 3VYN A; 5DUJ A; 5DCC A; 5DZP A; 4GSQ A; 4LPQ A; 5BUM A; 4JMN A; 2MTZ A; 3VYP A; 4QRB A; 1ZAT A; 3VYO A; 4QRA A; 2HKL A; 5LBG A; 4B8V A; 5DZJ A; 4XVO A; 4A1I A; 5K69 A; 4GSR A; 4A1K A; 5D7H A; 2LTF A; 4GSU A; 5E1G A; 4PXV A; 4A1J A; 1E0G A; 5DVP A;
#similar chains in the Genus database (?% sequence similarity) ...loading similar chains, please wait... #similar chains, but unknotted ...loading similar chains, please wait... #similar chains in the pdb database (?% sequence similarity) ...loading similar chains, please wait...
