2B13 | Genus

Total Genus 32

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	32
sequence length	131
structure length	131
Chain Sequence	HAKDASWLTSRKQLQPYGQYHGGGAHYGVDYAMPENSPVYSLTDGTVVQAGWSNYGGGNQVTIKEANSNNYQWYMHNNRLTVSAGDKVKAGDQIAYSGSTGNSTAPHVHFQRMSGGIGNQYAVDPTSYLQS

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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Viewer cachePut cache://localLOAD_/file/5cfca3ffe0f6540cec760cdb/pdb.gz

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The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/file/5cfca3ffe0f6540cec760cdb/pdb.gz): 1441 ms

reading 131 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

131 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:130});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

molecule tags	Hydrolase
source organism	Staphylococcus aureus
publication title	Crystal structures of active LytM. pubmed doi rcsb
molecule keywords	Glycyl-glycine endopeptidase lytM
total genus	32
structure length	131
sequence length	131
chains with identical sequence	B
ec nomenclature	ec 3.4.24.75: Lysostaphin.
pdb deposition date	2005-09-15

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01551	Peptidase_M23	Peptidase family M23

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
2.70.70.10	Mainly Beta	Distorted Sandwich	Glucose Permease (Domain IIA)	Glucose Permease (Domain IIA)	2b13A00

3IT7A 1O2FA 1GLEF 2F3GA 2B0PA 3CSQA 3SLUA 2GPRA 1QWYA 2B44A 4QP5A 4RNYA 1GLCF 4LXCA 2GU1A 3TUFB 1GPRA 4BH5A 1AX3A 4QPBA 3UZ0B 5B0HA 1GLBF 1GLDF 1F3ZA 3OURB 4ZYBA 1GLAF 4JBWM 1F3GA 3IT5A 2MP0B 4RNZA 2B13A 1GGRA 5KVPA 2HSIA 3NYYA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 3IT7 A;  1O2F A;  1GLE F;  2F3G A;  2B0P A;  3CSQ A;  3SLU A;  2GPR A;  1QWY A;  2B44 A;  4QP5 A;  4RNY A;  1GLC F;  4LXC A;  2GU1 A;  3TUF B;  1GPR A;  4BH5 A;  1AX3 A;  4QPB A;  3UZ0 B;  5B0H A;  1GLB F;  1GLD F;  1F3Z A;  3OUR B;  4ZYB A;  1GLA F;  4JBW M;  1F3G A;  3IT5 A;  2MP0 B;  4RNZ A;  2B13 A;  1GGR A;  5KVP A;  2HSI A;  3NYY A; 
#chains in the Genus database with same CATH topology
 3IT7 A;  1O2F A;  1GLE F;  2F3G A;  2B0P A;  3CSQ A;  3SLU A;  2GPR A;  1QWY A;  2B44 A;  4QP5 A;  4RNY A;  1GLC F;  4LXC A;  2GU1 A;  3TUF B;  1GPR A;  4BH5 A;  1AX3 A;  4QPB A;  3UZ0 B;  5B0H A;  1GLB F;  1GLD F;  1F3Z A;  3OUR B;  4ZYB A;  1GLA F;  4JBW M;  1F3G A;  3IT5 A;  2MP0 B;  4RNZ A;  2B13 A;  1GGR A;  5KVP A;  2HSI A;  3NYY A; 
#chains in the Genus database with same CATH homology
 3IT7 A;  1O2F A;  1GLE F;  2F3G A;  2B0P A;  3CSQ A;  3SLU A;  2GPR A;  1QWY A;  2B44 A;  4QP5 A;  4RNY A;  1GLC F;  4LXC A;  2GU1 A;  3TUF B;  1GPR A;  4BH5 A;  1AX3 A;  4QPB A;  3UZ0 B;  5B0H A;  1GLB F;  1GLD F;  1F3Z A;  3OUR B;  4ZYB A;  1GLA F;  4JBW M;  1F3G A;  3IT5 A;  2MP0 B;  4RNZ A;  2B13 A;  1GGR A;  5KVP A;  2HSI A;  3NYY 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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2B13A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations