3CPW | Genus

Total Genus 55

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	55
sequence length	194
structure length	194
Chain Sequence	ARSAYSYIRDAWKNPGDGQLAELQWQRQQEWRNEGAVERIERPTRLDKARSQGYKAKQGVIVARVSVRKGSARKRRHKAGRRSKRQGVTRITRRKDIQRVAEERASRTFPNLRVLNSYSVGQDGRQKWHEVILIDPNHPAIQNDDDLSWICADDQADRVFRGLTGAGRRNRGLSGKGKGSEKTRPSLRSNGGKG

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/5d1819e0746989f52cdfb3d2/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d1819e0746989f52cdfb3d2/pdb.gz): 991 ms

reading 194 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

194 atoms created

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

Time for creating model: 22 ms

Adding embedded #jmolscript: select ({0:193});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	Ribosome
publication title	Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit pubmed doi rcsb
molecule keywords	23S RIBOSOMAL RNA
total genus	55
structure length	194
sequence length	194
ec nomenclature
pdb deposition date	2008-04-01

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
L	PF00827	Ribosomal_L15e	Ribosomal L15

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.1120.10	Alpha Beta	3-Layer(aba) Sandwich	Ribosomal protein L15e	Ribosomal protein l15e	3cpwL00

2QA4M 1VQ8M 3G4SM 2OTLM 3CC7M 3I56M 1Q7YN 3CD6M 3CMAM 3CC2M 1VQKM 1VQPM 3CC4M 3CCQM 1K9MN 1NJIN 3I55M 1M1KN 1Q82N 1YITM 3CCRM 1N8RN 1VQMM 3CCMM 3CCLM 1QVGL 1QVFL 1YIJM 1W2BL 1JJ2L 3CXCL 3G6EM 1YI2M 3CCJM 1YJNM 1VQ9M 1YJWM 1K8AN 3CCSM 1Q81N 3CCUM 1VQ7M 1K73N 1KC8N 1VQLM 1Q86N 1VQNM 2QEXM 1YJ9M 1M90N 1VQ4M 3CPWL 1KQSL 1VQ5M 1YHQM 1VQ6M 3CCVM 1KD1N 1VQOM 3CCEM 2OTJM 3OW2L 3CMEM 3G71M 1S72M
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2QA4 M;  1VQ8 M;  3G4S M;  2OTL M;  3CC7 M;  3I56 M;  1Q7Y N;  3CD6 M;  3CMA M;  3CC2 M;  1VQK M;  1VQP M;  3CC4 M;  3CCQ M;  1K9M N;  1NJI N;  3I55 M;  1M1K N;  1Q82 N;  1YIT M;  3CCR M;  1N8R N;  1VQM M;  3CCM M;  3CCL M;  1QVG L;  1QVF L;  1YIJ M;  1W2B L;  1JJ2 L;  3CXC L;  3G6E M;  1YI2 M;  3CCJ M;  1YJN M;  1VQ9 M;  1YJW M;  1K8A N;  3CCS M;  1Q81 N;  3CCU M;  1VQ7 M;  1K73 N;  1KC8 N;  1VQL M;  1Q86 N;  1VQN M;  2QEX M;  1YJ9 M;  1M90 N;  1VQ4 M;  3CPW L;  1KQS L;  1VQ5 M;  1YHQ M;  1VQ6 M;  3CCV M;  1KD1 N;  1VQO M;  3CCE M;  2OTJ M;  3OW2 L;  3CME M;  3G71 M;  1S72 M; 
#chains in the Genus database with same CATH topology
 2QA4 M;  1VQ8 M;  3G4S M;  2OTL M;  3CC7 M;  3I56 M;  1Q7Y N;  3CD6 M;  3CMA M;  3CC2 M;  1VQK M;  1VQP M;  3CC4 M;  3CCQ M;  1K9M N;  1NJI N;  3I55 M;  1M1K N;  1Q82 N;  1YIT M;  3CCR M;  1N8R N;  1VQM M;  3CCM M;  3CCL M;  1QVG L;  1QVF L;  1YIJ M;  1W2B L;  1JJ2 L;  3CXC L;  3G6E M;  1YI2 M;  3CCJ M;  1YJN M;  1VQ9 M;  1YJW M;  1K8A N;  3CCS M;  1Q81 N;  3CCU M;  1VQ7 M;  1K73 N;  1KC8 N;  1VQL M;  1Q86 N;  1VQN M;  2QEX M;  1YJ9 M;  1M90 N;  1VQ4 M;  3CPW L;  1KQS L;  1VQ5 M;  1YHQ M;  1VQ6 M;  3CCV M;  1KD1 N;  1VQO M;  3CCE M;  2OTJ M;  3OW2 L;  3CME M;  3G71 M;  1S72 M; 
#chains in the Genus database with same CATH homology
 2QA4 M;  1VQ8 M;  3G4S M;  2OTL M;  3CC7 M;  3I56 M;  1Q7Y N;  3CD6 M;  3CMA M;  3CC2 M;  1VQK M;  1VQP M;  3CC4 M;  3CCQ M;  1K9M N;  1NJI N;  3I55 M;  1M1K N;  1Q82 N;  1YIT M;  3CCR M;  1N8R N;  1VQM M;  3CCM M;  3CCL M;  1QVG L;  1QVF L;  1YIJ M;  1W2B L;  1JJ2 L;  3CXC L;  3G6E M;  1YI2 M;  3CCJ M;  1YJN M;  1VQ9 M;  1YJW M;  1K8A N;  3CCS M;  1Q81 N;  3CCU M;  1VQ7 M;  1K73 N;  1KC8 N;  1VQL M;  1Q86 N;  1VQN M;  2QEX M;  1YJ9 M;  1M90 N;  1VQ4 M;  3CPW L;  1KQS L;  1VQ5 M;  1YHQ M;  1VQ6 M;  3CCV M;  1KD1 N;  1VQO M;  3CCE M;  2OTJ M;  3OW2 L;  3CME M;  3G71 M;  1S72 M;

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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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3CPWL

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations