1ZAT | Genus

Total Genus 62

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	62
sequence length	250
structure length	248
Chain Sequence	KEQLASMNAIANVKATYSINGETFQIPSSDIMSWLTYNDGKVDLDTEQVRQYVTDLGTKYNTSTNDTKFKSTKRGEVTVPVGTYSWTIQTDSETEALKKAILAGQDFTRSPIVQGGTTADHPLIEDTYIEVDLENQHMWYYKDGKVALETDIVSGKPTTPTPAGVFYVWNKEEDATLKGTNGTPYESPVNYWMPIDWTGVGIHDSDWQPEYGGDLWKTRGSHGCINTPPSVMKELFGMVEKGTPVLVF

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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Time for openFile(/file/5cfc8a4a2987dda4bf0c29f8/pdb.gz): 1796 ms

reading 248 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

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

Default Van der Waals type for model set to Jmol

248 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:247});backbone only;select *;

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

Chord Diagram

molecule tags	Transferase
source organism	Enterococcus faecium
publication title	Crystal Structure of a Novel beta-Lactam-insensitive Peptidoglycan Transpeptidase. pubmed doi rcsb
molecule keywords	L,D-transpeptidase
total genus	62
structure length	248
sequence length	250
ec nomenclature
pdb deposition date	2005-04-07

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
1.10.269.20	Mainly Alpha	Orthogonal Bundle	Adenovirus Single-stranded Dna-binding Protein, domain 1	Adenovirus Single-stranded Dna-binding Protein, domain 1	1zatA01
2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	1zatA02

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

4GSQA 4QRBA 1ADUA 3U1PA 3TURA 5DCCA 1ZATA 5E51A 5DC2A 5DZPA 3VYNA 1ANVA 3ZQDA 4LZHA 5LB1A 4A52A 3VYOA 4QR7A 3VYPA 2HKLA 5DZJA 4A1IA 4HUCA 4JMNA 4ZFQA 4QRAA 3U1QA 5DUJA 2MTZA 4A1JA 3VAEA 4A1KA 4GSRA 2WAZX 5E1IA 1ADVA 5E5LA 5D7HA 5DVPA 5LBGA 4Z7AA 2WB0X 4XVOA 5K69A 1Y7MA 3ZGPA 5E1GA 4QTFA 4GSUA 4JMXA 4LPQA 4K73A 5DU7A 3ZG4A 3TX4A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4GSQ A;  4QRB A;  3U1P A;  3TUR A;  5DCC A;  1ZAT A;  5E51 A;  5DC2 A;  5DZP A;  3VYN A;  3ZQD A;  4LZH A;  5LB1 A;  4A52 A;  3VYO A;  4QR7 A;  3VYP A;  2HKL A;  5DZJ A;  4A1I A;  4HUC A;  4JMN A;  4ZFQ A;  4QRA A;  3U1Q A;  5DUJ A;  2MTZ A;  4A1J A;  3VAE A;  4A1K A;  4GSR A;  5E1I A;  5E5L A;  5D7H A;  5DVP A;  5LBG A;  4Z7A A;  4XVO A;  5K69 A;  1Y7M A;  3ZGP A;  5E1G A;  4QTF A;  4GSU A;  4JMX A;  4LPQ A;  4K73 A;  5DU7 A;  3ZG4 A;  3TX4 A; 
#chains in the Genus database with same CATH topology
 4GSQ A;  4QRB A;  1ADU A;  3U1P A;  3TUR A;  5DCC A;  1ZAT A;  5E51 A;  5DC2 A;  5DZP A;  3VYN A;  1ANV A;  3ZQD A;  4LZH A;  5LB1 A;  4A52 A;  3VYO A;  4QR7 A;  3VYP A;  2HKL A;  5DZJ A;  4A1I A;  4HUC A;  4JMN A;  4ZFQ A;  4QRA A;  3U1Q A;  5DUJ A;  2MTZ A;  4A1J A;  3VAE A;  4A1K A;  4GSR A;  2WAZ X;  5E1I A;  1ADV A;  5E5L A;  5D7H A;  5DVP A;  5LBG A;  4Z7A A;  2WB0 X;  4XVO A;  5K69 A;  1Y7M A;  3ZGP A;  5E1G A;  4QTF A;  4GSU A;  4JMX A;  4LPQ A;  4K73 A;  5DU7 A;  3ZG4 A;  3TX4 A; 
#chains in the Genus database with same CATH homology
 4GSQ A;  4QRB A;  3U1P A;  3TUR A;  5DCC A;  1ZAT A;  5E51 A;  5DC2 A;  5DZP A;  3VYN A;  3ZQD A;  4LZH A;  5LB1 A;  4A52 A;  3VYO A;  4QR7 A;  3VYP A;  2HKL A;  5DZJ A;  4A1I A;  4HUC A;  4JMN A;  4ZFQ A;  4QRA A;  3U1Q A;  5DUJ A;  2MTZ A;  4A1J A;  3VAE A;  4A1K A;  4GSR A;  5E1I A;  5E5L A;  5D7H A;  5DVP A;  5LBG A;  4Z7A A;  4XVO A;  5K69 A;  1Y7M A;  3ZGP A;  5E1G A;  4QTF A;  4GSU A;  4JMX A;  4LPQ A;  4K73 A;  5DU7 A;  3ZG4 A;  3TX4 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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1ZATA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations