3ZQD | Genus

Total Genus 37

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	37
sequence length	169
structure length	169
Chain Sequence	GRKLLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINRGS

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 169 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

169 atoms created

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

Time for creating model: 20 ms

Adding embedded #jmolscript: select ({0:168});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	Bacillus subtilis subsp. subtilis
publication title	Dynamics Induced by Beta-Lactam Antibiotics in the Active Site of Bacillus subtilis L,D-Transpeptidase. pubmed doi rcsb
molecule keywords	L, D-TRANSPEPTIDASE YKUD
total genus	37
structure length	169
sequence length	169
ec nomenclature
pdb deposition date	2011-06-09

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01476	LysM	LysM domain
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	3zqdA02
3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D; Chain A	LysM domain	3zqdA01

3VAEA 4A1IA 1E0GA 5DZPA 4JMNA 4QRBA 1Y7MA 2LTFA 1ZATA 3VYOA 3ZGPA 4PXVA 5C8PA 5DCCA 5E5LA 5E1GA 4GSQA 3ZQDA 3VYPA 3TURA 3U1PA 3TX4A 4B9HA 3U1QA 5BUMA 4K73A 2MTZA 5E1IA 5LBGA 5DVPA 4HUCA 5DUJA 3VYNA 4QRAA 5C8QB 5K69A 4XVOA 4LPQA 2L9YA 5C8OA 4ZFQA 4A1KA 4LZHA 5DZJA 3ZG4A 4GSUA 2DJPA 5DU7A 5E51A 2HKLA 2MKXA 4B8VA 5K2LA 4JMXA 4GSRA 4Z7AA 5DC2A 4A52A 5D7HA 5LB1A 4A1JA 4QTFA 4QR7A
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3VAE A;  4A1I A;  1E0G A;  5DZP A;  4JMN A;  4QRB A;  1Y7M A;  2LTF A;  1ZAT A;  3VYO A;  3ZGP A;  4PXV A;  5C8P A;  5DCC A;  5E5L A;  5E1G A;  4GSQ A;  3ZQD A;  3VYP A;  3TUR A;  3U1P A;  3TX4 A;  4B9H A;  3U1Q A;  5BUM A;  4K73 A;  2MTZ A;  5E1I A;  5LBG A;  5DVP A;  4HUC A;  5DUJ A;  3VYN A;  4QRA A;  5C8Q B;  5K69 A;  4XVO A;  4LPQ A;  2L9Y A;  5C8O A;  4ZFQ A;  4A1K A;  4LZH A;  5DZJ A;  3ZG4 A;  4GSU A;  2DJP A;  5DU7 A;  5E51 A;  2HKL A;  2MKX A;  4B8V A;  5K2L A;  4JMX A;  4GSR A;  4Z7A A;  5DC2 A;  4A52 A;  5D7H A;  5LB1 A;  4A1J A;  4QTF A;  4QR7 A; 
#chains in the Genus database with same CATH topology
 3VAE A;  4A1I A;  1E0G A;  5DZP A;  4JMN A;  4QRB A;  1Y7M A;  2LTF A;  1ZAT A;  3VYO A;  3ZGP A;  4PXV A;  5C8P A;  5DCC A;  5E5L A;  5E1G A;  4GSQ A;  3ZQD A;  3VYP A;  3TUR A;  3U1P A;  3TX4 A;  4B9H A;  3U1Q A;  5BUM A;  4K73 A;  2MTZ A;  5E1I A;  5LBG A;  5DVP A;  4HUC A;  5DUJ A;  3VYN A;  4QRA A;  5C8Q B;  5K69 A;  4XVO A;  4LPQ A;  2L9Y A;  5C8O A;  4ZFQ A;  4A1K A;  4LZH A;  5DZJ A;  3ZG4 A;  4GSU A;  2DJP A;  5DU7 A;  5E51 A;  2HKL A;  2MKX A;  4B8V A;  5K2L A;  4JMX A;  4GSR A;  4Z7A A;  5DC2 A;  4A52 A;  5D7H A;  5LB1 A;  4A1J A;  4QTF A;  4QR7 A; 
#chains in the Genus database with same CATH homology
 3VAE A;  4A1I A;  1E0G A;  5DZP A;  4JMN A;  4QRB A;  1Y7M A;  2LTF A;  1ZAT A;  3VYO A;  3ZGP A;  4PXV A;  5C8P A;  5DCC A;  5E5L A;  5E1G A;  4GSQ A;  3ZQD A;  3VYP A;  3TUR A;  3U1P A;  3TX4 A;  4B9H A;  3U1Q A;  5BUM A;  4K73 A;  2MTZ A;  5E1I A;  5LBG A;  5DVP A;  4HUC A;  5DUJ A;  3VYN A;  4QRA A;  5C8Q B;  5K69 A;  4XVO A;  4LPQ A;  2L9Y A;  5C8O A;  4ZFQ A;  4A1K A;  4LZH A;  5DZJ A;  3ZG4 A;  4GSU A;  2DJP A;  5DU7 A;  5E51 A;  2HKL A;  2MKX A;  4B8V A;  5K2L A;  4JMX A;  4GSR A;  4Z7A A;  5DC2 A;  4A52 A;  5D7H A;  5LB1 A;  4A1J A;  4QTF A;  4QR7 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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3ZQDA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations