1VQ7J

The structure of the transition state analogue "dca" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 45
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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
45
sequence length
142
structure length
142
Chain Sequence
AEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPYDEDGEVLDGTSLDRLSNIKFVTLGEISETLGANKTW
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Ribosome
molecule keywords 23S ribosomal rna
publication title An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.
pubmed doi rcsb
total genus 45
structure length 142
sequence length 142
ec nomenclature
pdb deposition date 2004-12-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
J PF00572 Ribosomal_L13 Ribosomal protein L13
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.1180.10 Alpha Beta Alpha-Beta Complex Ribosomal Protein L13p; Chain: A; Ribosomal protein L13 1vq7J00
1KD1K 1YHQJ 1YIJJ 3PIOG 2ZJQG 1YJNJ 1KQSI 2QEXJ 1S72J 3CCVJ 4IOCG 1KC8K 3DLLG 3CC4J 2OTJJ 4IO9G 1VQ4J 1VQOJ 3G6EJ 1YJWJ 1VQ9J 1K73K 3CCRJ 1N8RK 3CMEJ 3I56J 3CCSJ 1W2BI 1Q82K 3CCJJ 3CCMJ 1VQLJ 3CCEJ 4IOAG 2OTLJ 1J3AA 1M90K 2ZJPG 3CPWI 4V19N 1VQPJ 1M1KK 1YI2J 3G4SJ 2ZJRG 1VQ8J 1YITJ 3CCQJ 1VQMJ 3CC7J 3CF5G 1Q86K 1NJIK 1VQ7J 1JJ2I 1QVGI 1VQ6J 3CC2J 1Q81K 3PIPG 1Q7YK 1VQ5J 2QA4J 3J7YK 1K8AK 3CMAJ 1QVFI 3CD6J 3CCLJ 3CCUJ 3CXCI 1VQKJ 3I55J 3OW2I 1K9MK 3G71J 1VQNJ 1YJ9J
chains in the Genus database with same CATH superfamily
1KD1K 1YHQJ 1YIJJ 3PIOG 2ZJQG 1YJNJ 1KQSI 2QEXJ 1S72J 3CCVJ 4IOCG 1KC8K 3DLLG 3CC4J 2OTJJ 4IO9G 1VQ4J 1VQOJ 3G6EJ 1YJWJ 1VQ9J 1K73K 3CCRJ 1N8RK 3CMEJ 3I56J 3CCSJ 1W2BI 1Q82K 3CCJJ 3CCMJ 1VQLJ 3CCEJ 4IOAG 2OTLJ 1J3AA 1M90K 2ZJPG 3CPWI 4V19N 1VQPJ 1M1KK 1YI2J 3G4SJ 2ZJRG 1VQ8J 1YITJ 3CCQJ 1VQMJ 3CC7J 3CF5G 1Q86K 1NJIK 1VQ7J 1JJ2I 1QVGI 1VQ6J 3CC2J 1Q81K 3PIPG 1Q7YK 1VQ5J 2QA4J 3J7YK 1K8AK 3CMAJ 1QVFI 3CD6J 3CCLJ 3CCUJ 3CXCI 1VQKJ 3I55J 3OW2I 1K9MK 3G71J 1VQNJ 1YJ9J
chains in the Genus database with same CATH topology
1KD1K 1YHQJ 1YIJJ 3PIOG 2ZJQG 1YJNJ 1KQSI 2QEXJ 1S72J 3CCVJ 4IOCG 1KC8K 3DLLG 3CC4J 2OTJJ 4IO9G 1VQ4J 1VQOJ 3G6EJ 1YJWJ 1VQ9J 1K73K 3CCRJ 1N8RK 3CMEJ 3I56J 3CCSJ 1W2BI 1Q82K 3CCJJ 3CCMJ 1VQLJ 3CCEJ 4IOAG 2OTLJ 1J3AA 1M90K 2ZJPG 3CPWI 4V19N 1VQPJ 1M1KK 1YI2J 3G4SJ 2ZJRG 1VQ8J 1YITJ 3CCQJ 1VQMJ 3CC7J 3CF5G 1Q86K 1NJIK 1VQ7J 1JJ2I 1QVGI 1VQ6J 3CC2J 1Q81K 3PIPG 1Q7YK 1VQ5J 2QA4J 3J7YK 1K8AK 3CMAJ 1QVFI 3CD6J 3CCLJ 3CCUJ 3CXCI 1VQKJ 3I55J 3OW2I 1K9MK 3G71J 1VQNJ 1YJ9J
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1KD1 K;  1YHQ J;  1YIJ J;  3PIO G;  2ZJQ G;  1YJN J;  1KQS I;  2QEX J;  1S72 J;  3CCV J;  4IOC G;  1KC8 K;  3DLL G;  3CC4 J;  2OTJ J;  4IO9 G;  1VQ4 J;  1VQO J;  3G6E J;  1YJW J;  1VQ9 J;  1K73 K;  3CCR J;  1N8R K;  3CME J;  3I56 J;  3CCS J;  1W2B I;  1Q82 K;  3CCJ J;  3CCM J;  1VQL J;  3CCE J;  4IOA G;  2OTL J;  1J3A A;  1M90 K;  2ZJP G;  3CPW I;  4V19 N;  1VQP J;  1M1K K;  1YI2 J;  3G4S J;  2ZJR G;  1VQ8 J;  1YIT J;  3CCQ J;  1VQM J;  3CC7 J;  3CF5 G;  1Q86 K;  1NJI K;  1VQ7 J;  1JJ2 I;  1QVG I;  1VQ6 J;  3CC2 J;  1Q81 K;  3PIP G;  1Q7Y K;  1VQ5 J;  2QA4 J;  3J7Y K;  1K8A K;  3CMA J;  1QVF I;  3CD6 J;  3CCL J;  3CCU J;  3CXC I;  1VQK J;  3I55 J;  3OW2 I;  1K9M K;  3G71 J;  1VQN J;  1YJ9 J; 
#chains in the Genus database with same CATH topology
 1KD1 K;  1YHQ J;  1YIJ J;  3PIO G;  2ZJQ G;  1YJN J;  1KQS I;  2QEX J;  1S72 J;  3CCV J;  4IOC G;  1KC8 K;  3DLL G;  3CC4 J;  2OTJ J;  4IO9 G;  1VQ4 J;  1VQO J;  3G6E J;  1YJW J;  1VQ9 J;  1K73 K;  3CCR J;  1N8R K;  3CME J;  3I56 J;  3CCS J;  1W2B I;  1Q82 K;  3CCJ J;  3CCM J;  1VQL J;  3CCE J;  4IOA G;  2OTL J;  1J3A A;  1M90 K;  2ZJP G;  3CPW I;  4V19 N;  1VQP J;  1M1K K;  1YI2 J;  3G4S J;  2ZJR G;  1VQ8 J;  1YIT J;  3CCQ J;  1VQM J;  3CC7 J;  3CF5 G;  1Q86 K;  1NJI K;  1VQ7 J;  1JJ2 I;  1QVG I;  1VQ6 J;  3CC2 J;  1Q81 K;  3PIP G;  1Q7Y K;  1VQ5 J;  2QA4 J;  3J7Y K;  1K8A K;  3CMA J;  1QVF I;  3CD6 J;  3CCL J;  3CCU J;  3CXC I;  1VQK J;  3I55 J;  3OW2 I;  1K9M K;  3G71 J;  1VQN J;  1YJ9 J; 
#chains in the Genus database with same CATH homology
 1KD1 K;  1YHQ J;  1YIJ J;  3PIO G;  2ZJQ G;  1YJN J;  1KQS I;  2QEX J;  1S72 J;  3CCV J;  4IOC G;  1KC8 K;  3DLL G;  3CC4 J;  2OTJ J;  4IO9 G;  1VQ4 J;  1VQO J;  3G6E J;  1YJW J;  1VQ9 J;  1K73 K;  3CCR J;  1N8R K;  3CME J;  3I56 J;  3CCS J;  1W2B I;  1Q82 K;  3CCJ J;  3CCM J;  1VQL J;  3CCE J;  4IOA G;  2OTL J;  1J3A A;  1M90 K;  2ZJP G;  3CPW I;  4V19 N;  1VQP J;  1M1K K;  1YI2 J;  3G4S J;  2ZJR G;  1VQ8 J;  1YIT J;  3CCQ J;  1VQM J;  3CC7 J;  3CF5 G;  1Q86 K;  1NJI K;  1VQ7 J;  1JJ2 I;  1QVG I;  1VQ6 J;  3CC2 J;  1Q81 K;  3PIP G;  1Q7Y K;  1VQ5 J;  2QA4 J;  3J7Y K;  1K8A K;  3CMA J;  1QVF I;  3CD6 J;  3CCL J;  3CCU J;  3CXC I;  1VQK J;  3I55 J;  3OW2 I;  1K9M K;  3G71 J;  1VQN J;  1YJ9 J; 
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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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