1VQ4R

The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 39
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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
39
sequence length
150
structure length
150
Chain Sequence
GISYSVEADPDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFKQHNSGVGHKSKVDGWDAGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAHKVGEQQGRKPRAMGRASAWNSPQVDVELILEEP
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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 39
structure length 150
sequence length 150
ec nomenclature
pdb deposition date 2004-12-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
R PF00237 Ribosomal_L22 Ribosomal protein L22p/L17e
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.470.10 Alpha Beta Alpha-Beta Complex Ribosomal Protein L22; Chain A Ribosomal protein L22/L17 1vq4R00
1VQ9R 3CCSR 3J7YT 5GADT 5GAET 3OW2Q 3CC2R 5GAGT 3CC7R 4WCEP 3CMER 4UY8S 3CCER 1QVFQ 1JJ2Q 1VQKR 2ZJQP 1Q81S 1VQ4R 4WF9P 5JVGP 4WFAP 2ZJPP 5DM7P 3CD6R 1VQMR 3I56R 1VQ5R 1W2BQ 2OTJR 2ZJRP 1M1KS 3PIPP 3DLLP 1NJIS 1YI2R 1YIJR 4WFNP 3CMAR 1S72R 3CCMR 1Q7YS 1K9MS 3CCQR 1I4JA 5MLCU 1K8AS 5GAHT 1VQ6R 4WFBP 5DM6P 3G6ER 2OTLR 4U67P 3CCJR 3CCUR 1KQSQ 1Q82S 5H1SU 1VQ8R 3CCRR 3CC4R 2QA4R 1YJNR 1YJWR 3PIOP 2QEXR 4IOAP 1M90S 4IO9P 1YITR 3CPWQ 4V19W 1VQOR 3G71R 1N8RS 3CCVR 1KD1S 3CXCQ 1YJ9R 1VQNR 1YHQR 1K73S 1VQLR 1BXEA 1VQPR 1Q86S 3J7ZS 3I55R 5JVHP 1VQ7R 3CCLR 1KC8S 3G4SR 5HL7P 4IOCP 3CF5P 1QVGQ
chains in the Genus database with same CATH superfamily
1VQ9R 3CCSR 3J7YT 5GADT 5GAET 3OW2Q 3CC2R 5GAGT 3CC7R 4WCEP 3CMER 4UY8S 3CCER 1QVFQ 1JJ2Q 1VQKR 2ZJQP 1QR0A 1Q81S 1FTFA 1VQ4R 2JCAA 2CG5A 2JBZA 3NE1A 4WF9P 5JVGP 1F7LA 4WFAP 2ZJPP 5DM7P 3CD6R 1VQMR 3I56R 2BYDA 1VQ5R 1F80A 1W2BQ 2OTJR 2ZJRP 1M1KS 3PIPP 2D0OA 3DLLP 2WATA 1NJIS 1YI2R 1YIJR 4WFNP 3CMAR 1S72R 3CCMR 2WDOA 1Q7YS 2WASB 1K9MS 3CCQR 5CXDA 3H7QA 1I4JA 3NFDA 5MLCU 1NBWA 1K8AS 3HQJA 5GAHT 1VQ6R 4WFBP 5DM6P 3G6ER 2OTLR 4U67P 3CCJR 3CCUR 1KQSQ 2WDYA 1Q82S 5H1SU 1VQ8R 2D0PA 3CC4R 3CCRR 2QA4R 1YJNR 1YJWR 5CMOA 3PIOP 3NE9A 4DXEA 1FTHA 2QEXR 4MRTA 2WASA 4IOAP 1M90S 4IO9P 3NE3B 1YITR 1FTEA 2QG8A 3CPWQ 3QMNA 4V19W 1VQOR 3G71R 1N8RS 3CCVR 2C43A 1KD1S 1F7TA 3CXCQ 1YJ9R 1VQNR 4JM7A 1YHQR 1K73S 1VQLR 1BXEA 1VQPR 4HC6A 1Q86S 3J7ZS 3I55R 3HYKA 5JVHP 1VQ7R 3CCLR 3GWMA 2BDDA 2WDSA 1KC8S 3G4SR 5HL7P 4IOCP 3CF5P 1QVGQ
chains in the Genus database with same CATH topology
1VQ9R 3CCSR 3J7YT 5GADT 5GAET 3OW2Q 3CC2R 5GAGT 3CC7R 4WCEP 3CMER 4UY8S 3CCER 1QVFQ 1JJ2Q 1VQKR 2ZJQP 1Q81S 1VQ4R 4WF9P 5JVGP 4WFAP 2ZJPP 5DM7P 3CD6R 1VQMR 3I56R 1VQ5R 1W2BQ 2OTJR 2ZJRP 1M1KS 3PIPP 3DLLP 1NJIS 1YI2R 1YIJR 4WFNP 3CMAR 1S72R 3CCMR 1Q7YS 1K9MS 3CCQR 1I4JA 5MLCU 1K8AS 5GAHT 1VQ6R 4WFBP 5DM6P 3G6ER 2OTLR 4U67P 3CCJR 3CCUR 1KQSQ 1Q82S 5H1SU 1VQ8R 3CCRR 3CC4R 2QA4R 1YJNR 1YJWR 3PIOP 2QEXR 4IOAP 1M90S 4IO9P 1YITR 3CPWQ 4V19W 1VQOR 3G71R 1N8RS 3CCVR 1KD1S 3CXCQ 1YJ9R 1VQNR 1YHQR 1K73S 1VQLR 1BXEA 1VQPR 1Q86S 3J7ZS 3I55R 5JVHP 1VQ7R 3CCLR 1KC8S 3G4SR 5HL7P 4IOCP 3CF5P 1QVGQ
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1VQ9 R;  3CCS R;  3J7Y T;  5GAD T;  5GAE T;  3OW2 Q;  3CC2 R;  5GAG T;  3CC7 R;  4WCE P;  3CME R;  4UY8 S;  3CCE R;  1QVF Q;  1JJ2 Q;  1VQK R;  2ZJQ P;  1Q81 S;  1VQ4 R;  4WF9 P;  5JVG P;  4WFA P;  2ZJP P;  5DM7 P;  3CD6 R;  1VQM R;  3I56 R;  1VQ5 R;  1W2B Q;  2OTJ R;  2ZJR P;  1M1K S;  3PIP P;  3DLL P;  1NJI S;  1YI2 R;  1YIJ R;  4WFN P;  3CMA R;  1S72 R;  3CCM R;  1Q7Y S;  1K9M S;  3CCQ R;  1I4J A;  5MLC U;  1K8A S;  5GAH T;  1VQ6 R;  4WFB P;  5DM6 P;  3G6E R;  2OTL R;  4U67 P;  3CCJ R;  3CCU R;  1KQS Q;  1Q82 S;  5H1S U;  1VQ8 R;  3CCR R;  3CC4 R;  2QA4 R;  1YJN R;  1YJW R;  3PIO P;  2QEX R;  4IOA P;  1M90 S;  4IO9 P;  1YIT R;  3CPW Q;  4V19 W;  1VQO R;  3G71 R;  1N8R S;  3CCV R;  1KD1 S;  3CXC Q;  1YJ9 R;  1VQN R;  1YHQ R;  1K73 S;  1VQL R;  1BXE A;  1VQP R;  1Q86 S;  3J7Z S;  3I55 R;  5JVH P;  1VQ7 R;  3CCL R;  1KC8 S;  3G4S R;  5HL7 P;  4IOC P;  3CF5 P;  1QVG Q; 
#chains in the Genus database with same CATH topology
 1VQ9 R;  3CCS R;  3J7Y T;  5GAD T;  5GAE T;  3OW2 Q;  3CC2 R;  5GAG T;  3CC7 R;  4WCE P;  3CME R;  4UY8 S;  3CCE R;  1QVF Q;  1JJ2 Q;  1VQK R;  2ZJQ P;  1QR0 A;  1Q81 S;  1FTF A;  1VQ4 R;  2JCA A;  2CG5 A;  2JBZ A;  3NE1 A;  4WF9 P;  5JVG P;  1F7L A;  4WFA P;  2ZJP P;  5DM7 P;  3CD6 R;  1VQM R;  3I56 R;  2BYD A;  1VQ5 R;  1F80 A;  1W2B Q;  2OTJ R;  2ZJR P;  1M1K S;  3PIP P;  2D0O A;  3DLL P;  2WAT A;  1NJI S;  1YI2 R;  1YIJ R;  4WFN P;  3CMA R;  1S72 R;  3CCM R;  2WDO A;  1Q7Y S;  2WAS B;  1K9M S;  3CCQ R;  5CXD A;  3H7Q A;  1I4J A;  3NFD A;  5MLC U;  1NBW A;  1K8A S;  3HQJ A;  5GAH T;  1VQ6 R;  4WFB P;  5DM6 P;  3G6E R;  2OTL R;  4U67 P;  3CCJ R;  3CCU R;  1KQS Q;  2WDY A;  1Q82 S;  5H1S U;  1VQ8 R;  2D0P A;  3CC4 R;  3CCR R;  2QA4 R;  1YJN R;  1YJW R;  5CMO A;  3PIO P;  3NE9 A;  4DXE A;  1FTH A;  2QEX R;  4MRT A;  2WAS A;  4IOA P;  1M90 S;  4IO9 P;  3NE3 B;  1YIT R;  1FTE A;  2QG8 A;  3CPW Q;  3QMN A;  4V19 W;  1VQO R;  3G71 R;  1N8R S;  3CCV R;  2C43 A;  1KD1 S;  1F7T A;  3CXC Q;  1YJ9 R;  1VQN R;  4JM7 A;  1YHQ R;  1K73 S;  1VQL R;  1BXE A;  1VQP R;  4HC6 A;  1Q86 S;  3J7Z S;  3I55 R;  3HYK A;  5JVH P;  1VQ7 R;  3CCL R;  3GWM A;  2BDD A;  2WDS A;  1KC8 S;  3G4S R;  5HL7 P;  4IOC P;  3CF5 P;  1QVG Q; 
#chains in the Genus database with same CATH homology
 1VQ9 R;  3CCS R;  3J7Y T;  5GAD T;  5GAE T;  3OW2 Q;  3CC2 R;  5GAG T;  3CC7 R;  4WCE P;  3CME R;  4UY8 S;  3CCE R;  1QVF Q;  1JJ2 Q;  1VQK R;  2ZJQ P;  1Q81 S;  1VQ4 R;  4WF9 P;  5JVG P;  4WFA P;  2ZJP P;  5DM7 P;  3CD6 R;  1VQM R;  3I56 R;  1VQ5 R;  1W2B Q;  2OTJ R;  2ZJR P;  1M1K S;  3PIP P;  3DLL P;  1NJI S;  1YI2 R;  1YIJ R;  4WFN P;  3CMA R;  1S72 R;  3CCM R;  1Q7Y S;  1K9M S;  3CCQ R;  1I4J A;  5MLC U;  1K8A S;  5GAH T;  1VQ6 R;  4WFB P;  5DM6 P;  3G6E R;  2OTL R;  4U67 P;  3CCJ R;  3CCU R;  1KQS Q;  1Q82 S;  5H1S U;  1VQ8 R;  3CCR R;  3CC4 R;  2QA4 R;  1YJN R;  1YJW R;  3PIO P;  2QEX R;  4IOA P;  1M90 S;  4IO9 P;  1YIT R;  3CPW Q;  4V19 W;  1VQO R;  3G71 R;  1N8R S;  3CCV R;  1KD1 S;  3CXC Q;  1YJ9 R;  1VQN R;  1YHQ R;  1K73 S;  1VQL R;  1BXE A;  1VQP R;  1Q86 S;  3J7Z S;  3I55 R;  5JVH P;  1VQ7 R;  3CCL R;  1KC8 S;  3G4S R;  5HL7 P;  4IOC P;  3CF5 P;  1QVG Q; 
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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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