3ZGP | Genus

Total Genus 18

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

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

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The Resolver thinks Pdb

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reading 129 atoms

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129 atoms created

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

molecule tags	Transferase
source organism	Enterococcus faecium
publication title	The Structure of Enterococcus Faecium L,D---Transpeptidase Acylated by Ertapenem Provides Insight Into the Inactivation Mechanism. pubmed doi rcsb
molecule keywords	ERFK/YBIS/YCFS/YNHG
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	Class	Architecture	Topology	Homology	Domain
2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	3zgpA00

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations