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 |
64
|
sequence length |
204
|
structure length |
204
|
Chain Sequence |
EPPAPQYPQRGSTGPEVLALQQRLMDLGYFILKADGDYGWATQQAVWAFQKAAGLYRDGVVGPQTQAALDAGYRPTPRSSSGKVVEIDLDKQILLAVEDGRVVRIINASSGNGETYEAKGRTYRATTPRGDFAVYMQRDGMHSSTLELGDMWRPKYFRGGYAVHGSSSIPTYPASHGCVRVSNAAMNWLWDSWGMPIGTRVLLY
|
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 |
Crystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894
rcsb |
| molecule tags |
Transferase
|
| source organism |
Xylanimonas cellulosilytica
|
| molecule keywords |
ErfK/YbiS/YcfS/YnhG family protein
|
| total genus |
64
|
| structure length |
204
|
| sequence length |
204
|
| ec nomenclature | |
| pdb deposition date | 2013-07-16 |
| chain | Pfam Accession Code | Pfam Family Identifier | Pfam Description |
|---|---|---|---|
| A | PF01471 | PG_binding_1 | Putative peptidoglycan binding 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 Alpha | Orthogonal Bundle | Muramoyl-pentapeptide Carboxypeptidase; domain 1 | PGBD-like superfamily/PGBD | ||
| Mainly Beta | Beta Barrel | L,D-transpeptidase catalytic domain-like | L,D-transpeptidase catalytic domain-like |
#chains in the Genus database with same CATH superfamily 5K69 A; 5LBG A; 4G54 A; 3U1Q A; 3VAE A; 5DZP A; 4QTF A; 2MTZ A; 4QRA A; 5E5L A; 4XVO A; 5E1I A; 3U1P A; 3BKH A; 2HKL A; 2WKX A; 5DC2 A; 4LPQ A; 3TUR A; 1EAK A; 3VYP A; 4A52 A; 4LZH A; 4BPA A; 4GSR A; 4A1J A; 2BH7 A; 4A1I A; 1ZAT A; 4JMX A; 4Z7A A; 4BJ4 A; 3D2Z A; 4GSU A; 5DVP A; 1LBU A; 5DZJ A; 3D2Y A; 4ZFQ A; 5LB1 A; 3TX4 A; 4K73 A; 4GSQ A; 4A1K A; 4BXD A; 3VYO A; 4BOL A; 4QR7 A; 3ZGP A; 3ZQD A; 5D7H A; 4HUC A; 3BKV A; 4BXE A; 5DCC A; 5DUJ A; 4QRB A; 5DU7 A; 4JMN A; 1Y7M A; 1L6J A; 5E51 A; 3VYN A; 4BXJ A; 5E1G A; 3ZG4 A; #chains in the Genus database with same CATH topology 5K69 A; 5LBG A; 4G54 A; 3U1Q A; 3VAE A; 5DZP A; 4QTF A; 2MTZ A; 4QRA A; 5E5L A; 4XVO A; 5E1I A; 3U1P A; 3BKH A; 2HKL A; 2WKX A; 5DC2 A; 4LPQ A; 3TUR A; 1EAK A; 3VYP A; 4A52 A; 4LZH A; 4BPA A; 4GSR A; 4A1J A; 2BH7 A; 4A1I A; 1ZAT A; 4JMX A; 4Z7A A; 4BJ4 A; 3D2Z A; 4GSU A; 5DVP A; 1LBU A; 5DZJ A; 3D2Y A; 4ZFQ A; 5LB1 A; 3TX4 A; 4K73 A; 4GSQ A; 4A1K A; 4BXD A; 3VYO A; 4BOL A; 4QR7 A; 3ZGP A; 3ZQD A; 5D7H A; 4HUC A; 3BKV A; 4BXE A; 5DCC A; 5DUJ A; 4QRB A; 5DU7 A; 4JMN A; 1Y7M A; 1L6J A; 5E51 A; 3VYN A; 4BXJ A; 5E1G A; 3ZG4 A; #chains in the Genus database with same CATH homology 5K69 A; 5LBG A; 4G54 A; 3U1Q A; 3VAE A; 5DZP A; 4QTF A; 2MTZ A; 4QRA A; 5E5L A; 4XVO A; 5E1I A; 3U1P A; 3BKH A; 2HKL A; 2WKX A; 5DC2 A; 4LPQ A; 3TUR A; 1EAK A; 3VYP A; 4A52 A; 4LZH A; 4BPA A; 4GSR A; 4A1J A; 2BH7 A; 4A1I A; 1ZAT A; 4JMX A; 4Z7A A; 4BJ4 A; 3D2Z A; 4GSU A; 5DVP A; 1LBU A; 5DZJ A; 3D2Y A; 4ZFQ A; 5LB1 A; 3TX4 A; 4K73 A; 4GSQ A; 4A1K A; 4BXD A; 3VYO A; 4BOL A; 4QR7 A; 3ZGP A; 3ZQD A; 5D7H A; 4HUC A; 3BKV A; 4BXE A; 5DCC A; 5DUJ A; 4QRB A; 5DU7 A; 4JMN A; 1Y7M A; 1L6J A; 5E51 A; 3VYN A; 4BXJ A; 5E1G A; 3ZG4 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...
