3ZG4 | Genus

Total Genus 22

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	22
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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1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

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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	22
structure length	129
sequence length	129
ec nomenclature	ec 2.3.2.12: Peptidyltransferase.
pdb deposition date	2012-12-14

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	3zg4A00

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

#chains in the Genus database with same CATH superfamily
 4A1I A;  5DVP A;  3VYN A;  4LPQ A;  5D7H A;  3ZGP A;  4K73 A;  5DU7 A;  1ZAT A;  5DZJ A;  4A52 A;  5K69 A;  3U1P A;  4QRA A;  2MTZ A;  4QRB A;  5E1I A;  4GSQ A;  4QR7 A;  3TUR A;  3VYP A;  5LB1 A;  4A1J A;  5DC2 A;  4QTF A;  2HKL A;  1Y7M A;  4XVO A;  5E51 A;  4GSU A;  5E5L A;  3U1Q A;  3VAE A;  5DZP A;  4ZFQ A;  4JMX A;  4GSR A;  3VYO A;  3TX4 A;  4JMN A;  4A1K A;  5DUJ A;  3ZG4 A;  5LBG A;  4LZH A;  5E1G A;  4HUC A;  3ZQD A;  4Z7A A;  5DCC A; 
#chains in the Genus database with same CATH topology
 4A1I A;  5DVP A;  3VYN A;  4LPQ A;  5D7H A;  3ZGP A;  4K73 A;  5DU7 A;  1ZAT A;  5DZJ A;  4A52 A;  5K69 A;  3U1P A;  4QRA A;  2MTZ A;  4QRB A;  5E1I A;  4GSQ A;  4QR7 A;  3TUR A;  3VYP A;  5LB1 A;  4A1J A;  5DC2 A;  4QTF A;  2HKL A;  1Y7M A;  4XVO A;  5E51 A;  4GSU A;  5E5L A;  3U1Q A;  3VAE A;  5DZP A;  4ZFQ A;  4JMX A;  4GSR A;  3VYO A;  3TX4 A;  4JMN A;  4A1K A;  5DUJ A;  3ZG4 A;  5LBG A;  4LZH A;  5E1G A;  4HUC A;  3ZQD A;  4Z7A A;  5DCC A; 
#chains in the Genus database with same CATH homology
 4A1I A;  5DVP A;  3VYN A;  4LPQ A;  5D7H A;  3ZGP A;  4K73 A;  5DU7 A;  1ZAT A;  5DZJ A;  4A52 A;  5K69 A;  3U1P A;  4QRA A;  2MTZ A;  4QRB A;  5E1I A;  4GSQ A;  4QR7 A;  3TUR A;  3VYP A;  5LB1 A;  4A1J A;  5DC2 A;  4QTF A;  2HKL A;  1Y7M A;  4XVO A;  5E51 A;  4GSU A;  5E5L A;  3U1Q A;  3VAE A;  5DZP A;  4ZFQ A;  4JMX A;  4GSR A;  3VYO A;  3TX4 A;  4JMN A;  4A1K A;  5DUJ A;  3ZG4 A;  5LBG A;  4LZH A;  5E1G A;  4HUC A;  3ZQD A;  4Z7A A;  5DCC 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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3ZG4A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations