3ZGPA

Nmr structure of the catalytic domain from e. faecium l,d- transpeptidase acylated by ertapenem
Total Genus 18
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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
18
sequence length
129
structure length
129
Chain Sequence
GHMEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNDDGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF
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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.

molecule tags Transferase
molecule keywords ERFK/YBIS/YCFS/YNHG
publication title The Structure of Enterococcus Faecium L,D---Transpeptidase Acylated by Ertapenem Provides Insight Into the Inactivation Mechanism.
pubmed doi rcsb
source organism Enterococcus faecium
total genus 18
structure length 129
sequence length 129
ec nomenclature ec 2.3.2.12: Peptidyltransferase.
pdb deposition date 2012-12-18

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
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 3zgpA00
5DUJA 5DCCA 4QR7A 2HKLA 3ZG4A 5K69A 4GSQA 4GSRA 5DU7A 5LB1A 5LBGA 3U1QA 4A1KA 4A1IA 1Y7MA 4A52A 5DZPA 5E1GA 5DZJA 5E5LA 4JMXA 3U1PA 4JMNA 1ZATA 4LPQA 3TURA 5E1IA 3TX4A 4GSUA 4QRBA 5E51A 3ZGPA 3ZQDA 4ZFQA 4LZHA 4Z7AA 5DC2A 4A1JA 4HUCA 4K73A 2MTZA 5DVPA 3VYPA 4QRAA 4QTFA 3VAEA 5D7HA 3VYOA 4XVOA 3VYNA
chains in the Genus database with same CATH superfamily
5DUJA 5DCCA 4QR7A 2HKLA 3ZG4A 5K69A 4GSQA 4GSRA 5DU7A 5LB1A 5LBGA 3U1QA 4A1KA 4A1IA 1Y7MA 4A52A 5DZPA 5E1GA 5DZJA 5E5LA 4JMXA 3U1PA 4JMNA 1ZATA 4LPQA 3TURA 5E1IA 3TX4A 4GSUA 4QRBA 5E51A 3ZGPA 3ZQDA 4ZFQA 4LZHA 4Z7AA 5DC2A 4A1JA 4HUCA 4K73A 2MTZA 5DVPA 3VYPA 4QRAA 4QTFA 3VAEA 5D7HA 3VYOA 4XVOA 3VYNA
chains in the Genus database with same CATH topology
5DUJA 5DCCA 4QR7A 2HKLA 3ZG4A 5K69A 4GSQA 4GSRA 5DU7A 5LB1A 5LBGA 3U1QA 4A1KA 4A1IA 1Y7MA 4A52A 5DZPA 5E1GA 5DZJA 5E5LA 4JMXA 3U1PA 4JMNA 1ZATA 4LPQA 3TURA 5E1IA 3TX4A 4GSUA 4QRBA 5E51A 3ZGPA 3ZQDA 4ZFQA 4LZHA 4Z7AA 5DC2A 4A1JA 4HUCA 4K73A 2MTZA 5DVPA 3VYPA 4QRAA 4QTFA 3VAEA 5D7HA 3VYOA 4XVOA 3VYNA
chains in the Genus database with same CATH homology


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