1VQMJ

The structure of the transition state analogue "dan" 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 1vqmJ00
3G71J 1VQ8J 2ZJRG 3CPWI 1NJIK 1K9MK 1QVGI 1Q7YK 3CD6J 2QA4J 3CCRJ 3DLLG 1YIJJ 1VQOJ 3CC2J 3I56J 1KD1K 1VQ9J 3PIPG 1VQKJ 1VQ5J 3CCMJ 3OW2I 1VQPJ 1YITJ 3CCJJ 4IO9G 2ZJPG 1YJWJ 1VQ4J 3CC7J 1VQMJ 1KC8K 1YJ9J 3CXCI 1K8AK 3CMAJ 1VQ7J 3PIOG 1N8RK 4IOCG 2ZJQG 3J7YK 3CC4J 1QVFI 1Q86K 3CF5G 1M90K 2QEXJ 1Q81K 3CMEJ 3I55J 1Q82K 1YJNJ 1YI2J 1VQLJ 1KQSI 1VQ6J 3CCQJ 3CCSJ 1VQNJ 3G4SJ 3CCVJ 3CCUJ 1W2BI 3G6EJ 3CCLJ 1J3AA 4IOAG 1JJ2I 1K73K 1S72J 4V19N 1M1KK 2OTJJ 1YHQJ 3CCEJ 2OTLJ
chains in the Genus database with same CATH superfamily
3G71J 1VQ8J 2ZJRG 3CPWI 1NJIK 1K9MK 1QVGI 1Q7YK 3CD6J 2QA4J 3CCRJ 3DLLG 1YIJJ 1VQOJ 3CC2J 3I56J 1KD1K 1VQ9J 3PIPG 1VQKJ 1VQ5J 3CCMJ 3OW2I 1VQPJ 1YITJ 3CCJJ 4IO9G 2ZJPG 1YJWJ 1VQ4J 3CC7J 1VQMJ 1KC8K 1YJ9J 3CXCI 1K8AK 3CMAJ 1VQ7J 3PIOG 1N8RK 4IOCG 2ZJQG 3J7YK 3CC4J 1QVFI 1Q86K 3CF5G 1M90K 2QEXJ 1Q81K 3CMEJ 3I55J 1Q82K 1YJNJ 1YI2J 1VQLJ 1KQSI 1VQ6J 3CCQJ 3CCSJ 1VQNJ 3G4SJ 3CCVJ 3CCUJ 1W2BI 3G6EJ 3CCLJ 1J3AA 4IOAG 1JJ2I 1K73K 1S72J 4V19N 1M1KK 2OTJJ 1YHQJ 3CCEJ 2OTLJ
chains in the Genus database with same CATH topology
3G71J 1VQ8J 2ZJRG 3CPWI 1NJIK 1K9MK 1QVGI 1Q7YK 3CD6J 2QA4J 3CCRJ 3DLLG 1YIJJ 1VQOJ 3CC2J 3I56J 1KD1K 1VQ9J 3PIPG 1VQKJ 1VQ5J 3CCMJ 3OW2I 1VQPJ 1YITJ 3CCJJ 4IO9G 2ZJPG 1YJWJ 1VQ4J 3CC7J 1VQMJ 1KC8K 1YJ9J 3CXCI 1K8AK 3CMAJ 1VQ7J 3PIOG 1N8RK 4IOCG 2ZJQG 3J7YK 3CC4J 1QVFI 1Q86K 3CF5G 1M90K 2QEXJ 1Q81K 3CMEJ 3I55J 1Q82K 1YJNJ 1YI2J 1VQLJ 1KQSI 1VQ6J 3CCQJ 3CCSJ 1VQNJ 3G4SJ 3CCVJ 3CCUJ 1W2BI 3G6EJ 3CCLJ 1J3AA 4IOAG 1JJ2I 1K73K 1S72J 4V19N 1M1KK 2OTJJ 1YHQJ 3CCEJ 2OTLJ
chains in the Genus database with same CATH homology


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