1YITW

Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui
Total Genus 47
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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
47
sequence length
154
structure length
154
Chain Sequence
MHALVQLRGEVNMHTDIQDTLEMLNIHHVNHCTLVPETDAYRGMVAKVNDFVAFGEPSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFALLSEETTLREQGLSPTLRLHPPRGGHDGVKHPVKEGGQLGKHDTEGIDDLLEAMR
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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 Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance.
pubmed doi rcsb
molecule tags Ribosome/antibiotic
molecule keywords 23S RIBOSOMAL RNA
total genus 47
structure length 154
sequence length 154
ec nomenclature
pdb deposition date 2005-01-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
W PF00327 Ribosomal_L30 Ribosomal protein L30p/L7e
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.15.30 Mainly Alpha Orthogonal Bundle 3-methyladenine DNA Glycosylase II; Chain A, domain 3 3-methyladenine DNA Glycosylase II; Chain A, domain 3 1yitW02
3.30.1390.20 Alpha Beta 2-Layer Sandwich Ribosomal Protein L30; Chain: A, Ribosomal protein L30, ferredoxin-like fold domain 1yitW01
3I55W 4WF9W 3I56W 1YI2W 3CC2W 1K9MX 1Q86X 1VQLW 1W2BV 3G4SW 1VQ5W 3PIPW 5GAGa 3J7ZZ 1YITW 3CCJW 2QA4W 1Q81X 4WFNW 1YHQW 2QEXW 3CCLW 4UY8Z 3CD6W 2ZJQW 1VQPW 3PIOW 1VQ9W 5GAEa 1KQSV 2OTLW 1QVFV 1Q82X 4IOAW 1VQKW 3CCQW 5JVHW 3G6EW 1VQNW 1YIJW 3CCMW 1KD1X 5GAHa 4WFBW 4IOCW 4WCEW 2OTJW 3CCSW 5DM7W 3CXCV 3CCUW 1K73X 1S72W 2ZJPW 4U67W 3DLLW 3CC4W 4IO9W 1VQ6W 2ZJRW 1QVGV 5GADa 1YJNW 4WFAW 1VQ7W 1YJWW 5HL7W 1VQ8W 5DM6W 5JVGW 1YJ9W 3OW2V 1N8RX 1JJ2V 1VQ4W 3CF5W 1VQOW 3G71W 1VQMW 3CMEW 1Q7YX 1BXYA 3CCVW 1K8AX 3CPWV 1NJIX 1M1KX 1KC8X 3CCRW 3CCEW 3CMAW 1M90X 3CC7W
chains in the Genus database with same CATH superfamily
3I55W 4WF9W 3I56W 1YI2W 3ZG0A 3CC2W 1K9MX 1Q86X 3DNJA 1VQLW 3D3IA 5M1AA 4CPKA 1W2BV 2WA8A 5CA3A 3G4SW 1R6OC 1MWRA 1VQ5W 2W9RA 3PIPW 3O2OA 1MWSA 5GAGa 1MWTA 3W7SA 3J7ZZ 1YITW 3CCJW 2QA4W 1Q81X 4WFNW 1YHQW 2QEXW 3CCLW 4UY8Z 3CD6W 4YJXA 2ZJQW 4YKAA 3GQ1A 1VQPW 3PIOW 1VQ9W 5GAEa 1MWUA 1KQSV 3O1FA 5M18A 2OTLW 1QVFV 1DD4A 1Q82X 4CJNA 4IOAW 3W7WA 1VQKW 3CCQW 5JVHW 3G6EW 1VQNW 1YIJW 3CCMW 1KD1X 5GAHa 4WFBW 4IOCW 4WCEW 2OTJW 3CCSW 5DM7W 3O2BA 3ZFZA 3CXCV 3CCUW 3G1BA 1K73X 3W7UA 3ZG5A 1S72W 2ZJPW 3G19A 4U67W 3DLLW 3CC4W 4IO9W 1VQ6W 1CTFA 2ZJRW 1QVGV 4YJMA 1VQQA 5GADa 1YJNW 3O2HA 4WFAW 1VQ7W 1YJWW 5HL7W 1VQ8W 3W7TA 5DM6W 5JVGW 1YJ9W 3OW2V 1N8RX 4BL3A 1JJ2V 1RQUA 4C1NA 1VQ4W 5GW7A 3CF5W 1RQVA 1MBVB 4DKIA 1VQOW 2WA9A 1RQSA 3G71W 3W7XA 1VQMW 3CMEW 1MBXC 1Q7YX 5M19A 1BXYA 3CCVW 1K8AX 3CPWV 1NJIX 3G3PA 3GW1A 1M1KX 1R6QC 1LZWA 1KC8X 3CCRW 3CCEW 1MBUC 3CMAW 1MG9A 4BL2A 1M90X 3GQ0A 3O1FB 3CC7W 1DD3A
chains in the Genus database with same CATH topology
3I55W 4WF9W 3I56W 1YI2W 3CC2W 1K9MX 1Q86X 1VQLW 1W2BV 3G4SW 1VQ5W 3PIPW 5GAGa 3J7ZZ 1YITW 3CCJW 2QA4W 1Q81X 4WFNW 1YHQW 2QEXW 3CCLW 4UY8Z 3CD6W 2ZJQW 1VQPW 3PIOW 1VQ9W 5GAEa 1KQSV 2OTLW 1QVFV 1Q82X 4IOAW 1VQKW 3CCQW 5JVHW 3G6EW 1VQNW 1YIJW 3CCMW 1KD1X 5GAHa 4WFBW 4IOCW 4WCEW 2OTJW 3CCSW 5DM7W 3CXCV 3CCUW 1K73X 1S72W 2ZJPW 4U67W 3DLLW 3CC4W 4IO9W 1VQ6W 2ZJRW 1QVGV 5GADa 1YJNW 4WFAW 1VQ7W 1YJWW 5HL7W 1VQ8W 5DM6W 5JVGW 1YJ9W 3OW2V 1N8RX 1JJ2V 4C1NA 1VQ4W 3CF5W 1VQOW 3G71W 1VQMW 3CMEW 1Q7YX 1BXYA 3CCVW 1K8AX 3CPWV 1NJIX 1M1KX 1KC8X 3CCRW 3CCEW 3CMAW 1M90X 3CC7W
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3I55 W;  4WF9 W;  3I56 W;  1YI2 W;  3CC2 W;  1K9M X;  1Q86 X;  1VQL W;  1W2B V;  3G4S W;  1VQ5 W;  3PIP W;  5GAG a;  3J7Z Z;  1YIT W;  3CCJ W;  2QA4 W;  1Q81 X;  4WFN W;  1YHQ W;  2QEX W;  3CCL W;  4UY8 Z;  3CD6 W;  2ZJQ W;  1VQP W;  3PIO W;  1VQ9 W;  5GAE a;  1KQS V;  2OTL W;  1QVF V;  1Q82 X;  4IOA W;  1VQK W;  3CCQ W;  5JVH W;  3G6E W;  1VQN W;  1YIJ W;  3CCM W;  1KD1 X;  5GAH a;  4WFB W;  4IOC W;  4WCE W;  2OTJ W;  3CCS W;  5DM7 W;  3CXC V;  3CCU W;  1K73 X;  1S72 W;  2ZJP W;  4U67 W;  3DLL W;  3CC4 W;  4IO9 W;  1VQ6 W;  2ZJR W;  1QVG V;  5GAD a;  1YJN W;  4WFA W;  1VQ7 W;  1YJW W;  5HL7 W;  1VQ8 W;  5DM6 W;  5JVG W;  1YJ9 W;  3OW2 V;  1N8R X;  1JJ2 V;  1VQ4 W;  3CF5 W;  1VQO W;  3G71 W;  1VQM W;  3CME W;  1Q7Y X;  1BXY A;  3CCV W;  1K8A X;  3CPW V;  1NJI X;  1M1K X;  1KC8 X;  3CCR W;  3CCE W;  3CMA W;  1M90 X;  3CC7 W; 
#chains in the Genus database with same CATH topology
 3I55 W;  4WF9 W;  3I56 W;  1YI2 W;  3ZG0 A;  3CC2 W;  1K9M X;  1Q86 X;  3DNJ A;  1VQL W;  3D3I A;  5M1A A;  4CPK A;  1W2B V;  2WA8 A;  5CA3 A;  3G4S W;  1R6O C;  1MWR A;  1VQ5 W;  2W9R A;  3PIP W;  3O2O A;  1MWS A;  5GAG a;  1MWT A;  3W7S A;  3J7Z Z;  1YIT W;  3CCJ W;  2QA4 W;  1Q81 X;  4WFN W;  1YHQ W;  2QEX W;  3CCL W;  4UY8 Z;  3CD6 W;  4YJX A;  2ZJQ W;  4YKA A;  3GQ1 A;  1VQP W;  3PIO W;  1VQ9 W;  5GAE a;  1MWU A;  1KQS V;  3O1F A;  5M18 A;  2OTL W;  1QVF V;  1DD4 A;  1Q82 X;  4CJN A;  4IOA W;  3W7W A;  1VQK W;  3CCQ W;  5JVH W;  3G6E W;  1VQN W;  1YIJ W;  3CCM W;  1KD1 X;  5GAH a;  4WFB W;  4IOC W;  4WCE W;  2OTJ W;  3CCS W;  5DM7 W;  3O2B A;  3ZFZ A;  3CXC V;  3CCU W;  3G1B A;  1K73 X;  3W7U A;  3ZG5 A;  1S72 W;  2ZJP W;  3G19 A;  4U67 W;  3DLL W;  3CC4 W;  4IO9 W;  1VQ6 W;  1CTF A;  2ZJR W;  1QVG V;  4YJM A;  1VQQ A;  5GAD a;  1YJN W;  3O2H A;  4WFA W;  1VQ7 W;  1YJW W;  5HL7 W;  1VQ8 W;  3W7T A;  5DM6 W;  5JVG W;  1YJ9 W;  3OW2 V;  1N8R X;  4BL3 A;  1JJ2 V;  1RQU A;  4C1N A;  1VQ4 W;  5GW7 A;  3CF5 W;  1RQV A;  1MBV B;  4DKI A;  1VQO W;  2WA9 A;  1RQS A;  3G71 W;  3W7X A;  1VQM W;  3CME W;  1MBX C;  1Q7Y X;  5M19 A;  1BXY A;  3CCV W;  1K8A X;  3CPW V;  1NJI X;  3G3P A;  3GW1 A;  1M1K X;  1R6Q C;  1LZW A;  1KC8 X;  3CCR W;  3CCE W;  1MBU C;  3CMA W;  1MG9 A;  4BL2 A;  1M90 X;  3GQ0 A;  3O1F B;  3CC7 W;  1DD3 A; 
#chains in the Genus database with same CATH homology
 3I55 W;  4WF9 W;  3I56 W;  1YI2 W;  3CC2 W;  1K9M X;  1Q86 X;  1VQL W;  1W2B V;  3G4S W;  1VQ5 W;  3PIP W;  5GAG a;  3J7Z Z;  1YIT W;  3CCJ W;  2QA4 W;  1Q81 X;  4WFN W;  1YHQ W;  2QEX W;  3CCL W;  4UY8 Z;  3CD6 W;  2ZJQ W;  1VQP W;  3PIO W;  1VQ9 W;  5GAE a;  1KQS V;  2OTL W;  1QVF V;  1Q82 X;  4IOA W;  1VQK W;  3CCQ W;  5JVH W;  3G6E W;  1VQN W;  1YIJ W;  3CCM W;  1KD1 X;  5GAH a;  4WFB W;  4IOC W;  4WCE W;  2OTJ W;  3CCS W;  5DM7 W;  3CXC V;  3CCU W;  1K73 X;  1S72 W;  2ZJP W;  4U67 W;  3DLL W;  3CC4 W;  4IO9 W;  1VQ6 W;  2ZJR W;  1QVG V;  5GAD a;  1YJN W;  4WFA W;  1VQ7 W;  1YJW W;  5HL7 W;  1VQ8 W;  5DM6 W;  5JVG W;  1YJ9 W;  3OW2 V;  1N8R X;  1JJ2 V;  4C1N A;  1VQ4 W;  3CF5 W;  1VQO W;  3G71 W;  1VQM W;  3CME W;  1Q7Y X;  1BXY A;  3CCV W;  1K8A X;  3CPW V;  1NJI X;  1M1K X;  1KC8 X;  3CCR W;  3CCE W;  3CMA W;  1M90 X;  3CC7 W; 
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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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