1VQ5R

The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 37
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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
37
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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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
molecule tags Ribosome
molecule keywords 23S ribosomal rna
total genus 37
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 1vq5R00
3CCSR 1YIJR 1M1KS 4V19W 5H1SU 3CCQR 1Q86S 1I4JA 4WFNP 5JVGP 1VQNR 1VQ5R 1Q7YS 5DM7P 3J7ZS 3G71R 3I56R 3CCLR 1W2BQ 3G4SR 1YHQR 1S72R 1Q82S 4WFAP 1VQ8R 1YJ9R 5GAET 3I55R 4IOCP 3CCJR 3CCVR 1K8AS 3G6ER 3CXCQ 1VQ4R 1VQKR 5GAHT 3CD6R 5GAGT 2QEXR 1VQPR 1KD1S 2ZJQP 5JVHP 3CC2R 4WF9P 3PIOP 3CCER 3OW2Q 4IOAP 3CC4R 1N8RS 2ZJPP 3CMER 3CCMR 4WCEP 1YI2R 1JJ2Q 3CCUR 1VQMR 1YJWR 3CPWQ 5MLCU 4U67P 1K9MS 3PIPP 1KC8S 2QA4R 4UY8S 3J7YT 1Q81S 4IO9P 1QVGQ 3DLLP 1VQLR 5DM6P 1QVFQ 2ZJRP 1KQSQ 4WFBP 3CC7R 3CF5P 3CMAR 1YJNR 5GADT 2OTJR 1VQ7R 1M90S 1NJIS 1K73S 1VQOR 5HL7P 1VQ9R 1YITR 2OTLR 1BXEA 1VQ6R 3CCRR
chains in the Genus database with same CATH superfamily
3CCSR 1FTEA 1YIJR 1M1KS 4V19W 3NFDA 4JM7A 2D0PA 5H1SU 3CCQR 1Q86S 1I4JA 4WFNP 5JVGP 1VQNR 1FTFA 1VQ5R 1Q7YS 2WATA 3NE3B 5DM7P 4DXEA 3NE1A 3J7ZS 3G71R 3I56R 3CCLR 1W2BQ 3G4SR 1YHQR 2BYDA 3GWMA 1S72R 1Q82S 3H7QA 4WFAP 1VQ8R 1YJ9R 5GAET 3I55R 2C43A 2CG5A 4IOCP 3CCJR 5CXDA 3CCVR 1K8AS 4HC6A 1FTHA 3G6ER 3CXCQ 2WDOA 1VQ4R 1VQKR 5GAHT 3CD6R 2WDSA 3NE9A 5GAGT 2QEXR 1QR0A 1VQPR 2ZJQP 1KD1S 5JVHP 1F7TA 3CC2R 1F7LA 4WF9P 5CMOA 2WASA 1F80A 1NBWA 3PIOP 4MRTA 3CCER 3OW2Q 4IOAP 3CC4R 2D0OA 2WDYA 1N8RS 2ZJPP 2WASB 3CMER 3CCMR 4WCEP 1YI2R 1JJ2Q 3CCUR 1VQMR 1YJWR 3CPWQ 5MLCU 4U67P 1K9MS 3PIPP 1KC8S 2QA4R 4UY8S 3J7YT 3QMNA 1Q81S 4IO9P 1QVGQ 3HQJA 3DLLP 1VQLR 5DM6P 1QVFQ 2ZJRP 1KQSQ 4WFBP 2JBZA 3CC7R 2BDDA 2QG8A 3CF5P 3CMAR 1YJNR 5GADT 2OTJR 1VQ7R 1M90S 3HYKA 2JCAA 1NJIS 1K73S 1VQOR 5HL7P 1VQ9R 1YITR 2OTLR 1BXEA 1VQ6R 3CCRR
chains in the Genus database with same CATH topology
3CCSR 1YIJR 1M1KS 4V19W 5H1SU 3CCQR 1Q86S 1I4JA 4WFNP 5JVGP 1VQNR 1VQ5R 1Q7YS 5DM7P 3J7ZS 3G71R 3I56R 3CCLR 1W2BQ 3G4SR 1YHQR 1S72R 1Q82S 4WFAP 1VQ8R 1YJ9R 5GAET 3I55R 4IOCP 3CCJR 3CCVR 1K8AS 3G6ER 3CXCQ 1VQ4R 1VQKR 5GAHT 3CD6R 5GAGT 2QEXR 1VQPR 1KD1S 2ZJQP 5JVHP 3CC2R 4WF9P 3PIOP 3CCER 3OW2Q 4IOAP 3CC4R 1N8RS 2ZJPP 3CMER 3CCMR 4WCEP 1YI2R 1JJ2Q 3CCUR 1VQMR 1YJWR 3CPWQ 5MLCU 4U67P 1K9MS 3PIPP 1KC8S 2QA4R 4UY8S 3J7YT 1Q81S 4IO9P 1QVGQ 3DLLP 1VQLR 5DM6P 1QVFQ 2ZJRP 1KQSQ 4WFBP 3CC7R 3CF5P 3CMAR 1YJNR 5GADT 2OTJR 1VQ7R 1M90S 1NJIS 1K73S 1VQOR 5HL7P 1VQ9R 1YITR 2OTLR 1BXEA 1VQ6R 3CCRR
chains in the Genus database with same CATH homology


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