3CD6 | Genus

Total Genus 47

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	47
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/5d26412431fe448a3836d39e/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d26412431fe448a3836d39e/pdb.gz): 1710 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: 23 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	Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. pubmed doi rcsb
molecule keywords	50S ribosomal protein L2P
total genus	47
structure length	194
sequence length	194
ec nomenclature
pdb deposition date	2008-02-26

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
M	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	3cd6M00

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

#chains in the Genus database with same CATH superfamily
 3G6E M;  1YIT M;  1VQO M;  1QVG L;  3CCM M;  1VQM M;  1VQ8 M;  3CD6 M;  3CC7 M;  1VQP M;  3G4S M;  3CC4 M;  1YJN M;  3CCL M;  1VQ5 M;  1Q81 N;  1NJI N;  1KQS L;  1K73 N;  1VQ4 M;  1S72 M;  1YJ9 M;  1K9M N;  3CCQ M;  1VQ9 M;  3CCJ M;  3CCE M;  3CXC L;  1QVF L;  3G71 M;  2QEX M;  1K8A N;  1Q82 N;  3I56 M;  1YI2 M;  3CC2 M;  3CCU M;  3OW2 L;  1N8R N;  1YHQ M;  1VQ6 M;  1VQN M;  3CPW L;  1KC8 N;  1VQ7 M;  1W2B L;  3I55 M;  1Q86 N;  2OTJ M;  3CME M;  1Q7Y N;  3CCV M;  1M1K N;  1VQK M;  1VQL M;  1M90 N;  3CCS M;  1JJ2 L;  1YJW M;  1KD1 N;  3CMA M;  1YIJ M;  2OTL M;  3CCR M;  2QA4 M; 
#chains in the Genus database with same CATH topology
 3G6E M;  1YIT M;  1VQO M;  1QVG L;  3CCM M;  1VQM M;  1VQ8 M;  3CD6 M;  3CC7 M;  1VQP M;  3G4S M;  3CC4 M;  1YJN M;  3CCL M;  1VQ5 M;  1Q81 N;  1NJI N;  1KQS L;  1K73 N;  1VQ4 M;  1S72 M;  1YJ9 M;  1K9M N;  3CCQ M;  1VQ9 M;  3CCJ M;  3CCE M;  3CXC L;  1QVF L;  3G71 M;  2QEX M;  1K8A N;  1Q82 N;  3I56 M;  1YI2 M;  3CC2 M;  3CCU M;  3OW2 L;  1N8R N;  1YHQ M;  1VQ6 M;  1VQN M;  3CPW L;  1KC8 N;  1VQ7 M;  1W2B L;  3I55 M;  1Q86 N;  2OTJ M;  3CME M;  1Q7Y N;  3CCV M;  1M1K N;  1VQK M;  1VQL M;  1M90 N;  3CCS M;  1JJ2 L;  1YJW M;  1KD1 N;  3CMA M;  1YIJ M;  2OTL M;  3CCR M;  2QA4 M; 
#chains in the Genus database with same CATH homology
 3G6E M;  1YIT M;  1VQO M;  1QVG L;  3CCM M;  1VQM M;  1VQ8 M;  3CD6 M;  3CC7 M;  1VQP M;  3G4S M;  3CC4 M;  1YJN M;  3CCL M;  1VQ5 M;  1Q81 N;  1NJI N;  1KQS L;  1K73 N;  1VQ4 M;  1S72 M;  1YJ9 M;  1K9M N;  3CCQ M;  1VQ9 M;  3CCJ M;  3CCE M;  3CXC L;  1QVF L;  3G71 M;  2QEX M;  1K8A N;  1Q82 N;  3I56 M;  1YI2 M;  3CC2 M;  3CCU M;  3OW2 L;  1N8R N;  1YHQ M;  1VQ6 M;  1VQN M;  3CPW L;  1KC8 N;  1VQ7 M;  1W2B L;  3I55 M;  1Q86 N;  2OTJ M;  3CME M;  1Q7Y N;  3CCV M;  1M1K N;  1VQK M;  1VQL M;  1M90 N;  3CCS M;  1JJ2 L;  1YJW M;  1KD1 N;  3CMA M;  1YIJ M;  2OTL M;  3CCR M;  2QA4 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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3CD6M

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations