1VQ4J

The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 44
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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
44
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 Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.
pubmed doi rcsb
total genus 44
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 1vq4J00
1JJ2I 1VQ4J 1VQLJ 1K9MK 1M90K 1KC8K 3J7YK 3CF5G 1M1KK 1K8AK 1VQ7J 1VQPJ 3CXCI 2QA4J 3CCSJ 3CD6J 3G71J 3PIPG 1QVGI 3CCUJ 1Q7YK 1KD1K 1QVFI 3CMAJ 1N8RK 1J3AA 1YIJJ 3CCJJ 1YHQJ 4IOAG 2ZJRG 1VQKJ 1VQNJ 2QEXJ 3CCMJ 3G4SJ 3CC2J 3CCLJ 1Q82K 2ZJPG 1YJNJ 3PIOG 4IOCG 1S72J 3OW2I 3CC4J 1YJWJ 1VQMJ 1VQOJ 2OTJJ 3CCVJ 1KQSI 3CC7J 3DLLG 3CCEJ 3I56J 2OTLJ 3CCRJ 4IO9G 3G6EJ 1VQ6J 1VQ9J 1K73K 3I55J 1Q86K 1YJ9J 1VQ5J 1Q81K 1YITJ 2ZJQG 1YI2J 1NJIK 1VQ8J 3CPWI 3CCQJ 4V19N 3CMEJ 1W2BI
chains in the Genus database with same CATH superfamily
1JJ2I 1VQ4J 1VQLJ 1K9MK 1M90K 1KC8K 3J7YK 3CF5G 1M1KK 1K8AK 1VQ7J 1VQPJ 3CXCI 2QA4J 3CCSJ 3CD6J 3G71J 3PIPG 1QVGI 3CCUJ 1Q7YK 1KD1K 1QVFI 3CMAJ 1N8RK 1J3AA 1YIJJ 3CCJJ 1YHQJ 4IOAG 2ZJRG 1VQKJ 1VQNJ 2QEXJ 3CCMJ 3G4SJ 3CC2J 3CCLJ 1Q82K 2ZJPG 1YJNJ 3PIOG 4IOCG 1S72J 3OW2I 3CC4J 1YJWJ 1VQMJ 1VQOJ 2OTJJ 3CCVJ 1KQSI 3CC7J 3DLLG 3CCEJ 3I56J 2OTLJ 3CCRJ 4IO9G 3G6EJ 1VQ6J 1VQ9J 1K73K 3I55J 1Q86K 1YJ9J 1VQ5J 1Q81K 1YITJ 2ZJQG 1YI2J 1NJIK 1VQ8J 3CPWI 3CCQJ 4V19N 3CMEJ 1W2BI
chains in the Genus database with same CATH topology
1JJ2I 1VQ4J 1VQLJ 1K9MK 1M90K 1KC8K 3J7YK 3CF5G 1M1KK 1K8AK 1VQ7J 1VQPJ 3CXCI 2QA4J 3CCSJ 3CD6J 3G71J 3PIPG 1QVGI 3CCUJ 1Q7YK 1KD1K 1QVFI 3CMAJ 1N8RK 1J3AA 1YIJJ 3CCJJ 1YHQJ 4IOAG 2ZJRG 1VQKJ 1VQNJ 2QEXJ 3CCMJ 3G4SJ 3CC2J 3CCLJ 1Q82K 2ZJPG 1YJNJ 3PIOG 4IOCG 1S72J 3OW2I 3CC4J 1YJWJ 1VQMJ 1VQOJ 2OTJJ 3CCVJ 1KQSI 3CC7J 3DLLG 3CCEJ 3I56J 2OTLJ 3CCRJ 4IO9G 3G6EJ 1VQ6J 1VQ9J 1K73K 3I55J 1Q86K 1YJ9J 1VQ5J 1Q81K 1YITJ 2ZJQG 1YI2J 1NJIK 1VQ8J 3CPWI 3CCQJ 4V19N 3CMEJ 1W2BI
chains in the Genus database with same CATH homology


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