4LPQA

Crystal structure of the l,d-transpeptidase (residues 123-326) from xylanimonas cellulosilytica dsm 15894
Total Genus 64
Loading diagram...

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
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
molecule keywords ErfK/YbiS/YcfS/YnhG family protein
publication title Crystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894
rcsb
source organism Xylanimonas cellulosilytica
molecule tags Transferase
total genus 64
structure length 204
sequence length 204
ec nomenclature
pdb deposition date 2013-07-16

pfam database annotations

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
ClassArchitectureTopologyHomologyDomain
1.10.101.10 Mainly Alpha Orthogonal Bundle Muramoyl-pentapeptide Carboxypeptidase; domain 1 PGBD-like superfamily/PGBD 4lpqA01
2.40.440.10 Mainly Beta Beta Barrel L,D-transpeptidase catalytic domain-like L,D-transpeptidase catalytic domain-like 4lpqA02
3U1PA 3ZGPA 5DVPA 4GSUA 3VYPA 1Y7MA 3VYOA 4Z7AA 5K69A 4QRBA 4BXDA 3BKHA 3D2YA 1ZATA 5E51A 3ZQDA 1LBUA 2MTZA 3TURA 4QR7A 5D7HA 4QTFA 5LBGA 5DC2A 3VYNA 4JMNA 5E1IA 4LZHA 4A1JA 3ZG4A 4BXEA 4K73A 2HKLA 3TX4A 3U1QA 4ZFQA 5DZJA 1EAKA 5E5LA 4A1IA 5DU7A 3VAEA 4GSQA 4BOLA 4BXJA 5LB1A 4JMXA 4BPAA 5E1GA 1L6JA 5DZPA 4A1KA 5DCCA 4A52A 3D2ZA 4XVOA 4HUCA 2WKXA 4G54A 5DUJA 4GSRA 4BJ4A 3BKVA 4QRAA 4LPQA 2BH7A
chains in the Genus database with same CATH superfamily
3U1PA 3ZGPA 5DVPA 4GSUA 3VYPA 1Y7MA 3VYOA 4Z7AA 5K69A 4QRBA 4BXDA 3BKHA 3D2YA 1ZATA 5E51A 3ZQDA 1LBUA 2MTZA 3TURA 4QR7A 5D7HA 4QTFA 5LBGA 5DC2A 3VYNA 4JMNA 5E1IA 4LZHA 4A1JA 3ZG4A 4BXEA 4K73A 2HKLA 3TX4A 3U1QA 4ZFQA 5DZJA 1EAKA 5E5LA 4A1IA 5DU7A 3VAEA 4GSQA 4BOLA 4BXJA 5LB1A 4JMXA 4BPAA 5E1GA 1L6JA 5DZPA 4A1KA 5DCCA 4A52A 3D2ZA 4XVOA 4HUCA 2WKXA 4G54A 5DUJA 4GSRA 4BJ4A 3BKVA 4QRAA 4LPQA 2BH7A
chains in the Genus database with same CATH topology
3U1PA 3ZGPA 5DVPA 4GSUA 3VYPA 1Y7MA 3VYOA 4Z7AA 5K69A 4QRBA 4BXDA 3BKHA 3D2YA 1ZATA 5E51A 3ZQDA 1LBUA 2MTZA 3TURA 4QR7A 5D7HA 4QTFA 5LBGA 5DC2A 3VYNA 4JMNA 5E1IA 4LZHA 4A1JA 3ZG4A 4BXEA 4K73A 2HKLA 3TX4A 3U1QA 4ZFQA 5DZJA 1EAKA 5E5LA 4A1IA 5DU7A 3VAEA 4GSQA 4BOLA 4BXJA 5LB1A 4JMXA 4BPAA 5E1GA 1L6JA 5DZPA 4A1KA 5DCCA 4A52A 3D2ZA 4XVOA 4HUCA 2WKXA 4G54A 5DUJA 4GSRA 4BJ4A 3BKVA 4QRAA 4LPQA 2BH7A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3U1P A;  3ZGP A;  5DVP A;  4GSU A;  3VYP A;  1Y7M A;  3VYO A;  4Z7A A;  5K69 A;  4QRB A;  4BXD A;  3BKH A;  3D2Y A;  1ZAT A;  5E51 A;  3ZQD A;  1LBU A;  2MTZ A;  3TUR A;  4QR7 A;  5D7H A;  4QTF A;  5LBG A;  5DC2 A;  3VYN A;  4JMN A;  5E1I A;  4LZH A;  4A1J A;  3ZG4 A;  4BXE A;  4K73 A;  2HKL A;  3TX4 A;  3U1Q A;  4ZFQ A;  5DZJ A;  1EAK A;  5E5L A;  4A1I A;  5DU7 A;  3VAE A;  4GSQ A;  4BOL A;  4BXJ A;  5LB1 A;  4JMX A;  4BPA A;  5E1G A;  1L6J A;  5DZP A;  4A1K A;  5DCC A;  4A52 A;  3D2Z A;  4XVO A;  4HUC A;  2WKX A;  4G54 A;  5DUJ A;  4GSR A;  4BJ4 A;  3BKV A;  4QRA A;  4LPQ A;  2BH7 A; 
#chains in the Genus database with same CATH topology
 3U1P A;  3ZGP A;  5DVP A;  4GSU A;  3VYP A;  1Y7M A;  3VYO A;  4Z7A A;  5K69 A;  4QRB A;  4BXD A;  3BKH A;  3D2Y A;  1ZAT A;  5E51 A;  3ZQD A;  1LBU A;  2MTZ A;  3TUR A;  4QR7 A;  5D7H A;  4QTF A;  5LBG A;  5DC2 A;  3VYN A;  4JMN A;  5E1I A;  4LZH A;  4A1J A;  3ZG4 A;  4BXE A;  4K73 A;  2HKL A;  3TX4 A;  3U1Q A;  4ZFQ A;  5DZJ A;  1EAK A;  5E5L A;  4A1I A;  5DU7 A;  3VAE A;  4GSQ A;  4BOL A;  4BXJ A;  5LB1 A;  4JMX A;  4BPA A;  5E1G A;  1L6J A;  5DZP A;  4A1K A;  5DCC A;  4A52 A;  3D2Z A;  4XVO A;  4HUC A;  2WKX A;  4G54 A;  5DUJ A;  4GSR A;  4BJ4 A;  3BKV A;  4QRA A;  4LPQ A;  2BH7 A; 
#chains in the Genus database with same CATH homology
 3U1P A;  3ZGP A;  5DVP A;  4GSU A;  3VYP A;  1Y7M A;  3VYO A;  4Z7A A;  5K69 A;  4QRB A;  4BXD A;  3BKH A;  3D2Y A;  1ZAT A;  5E51 A;  3ZQD A;  1LBU A;  2MTZ A;  3TUR A;  4QR7 A;  5D7H A;  4QTF A;  5LBG A;  5DC2 A;  3VYN A;  4JMN A;  5E1I A;  4LZH A;  4A1J A;  3ZG4 A;  4BXE A;  4K73 A;  2HKL A;  3TX4 A;  3U1Q A;  4ZFQ A;  5DZJ A;  1EAK A;  5E5L A;  4A1I A;  5DU7 A;  3VAE A;  4GSQ A;  4BOL A;  4BXJ A;  5LB1 A;  4JMX A;  4BPA A;  5E1G A;  1L6J A;  5DZP A;  4A1K A;  5DCC A;  4A52 A;  3D2Z A;  4XVO A;  4HUC A;  2WKX A;  4G54 A;  5DUJ A;  4GSR A;  4BJ4 A;  3BKV A;  4QRA A;  4LPQ A;  2BH7 A; 
...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

 
#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...