1VQ4W

The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 50
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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
50
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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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 50
structure length 154
sequence length 154
ec nomenclature
pdb deposition date 2004-12-16

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 1vq4W02
3.30.1390.20 Alpha Beta 2-Layer Sandwich Ribosomal Protein L30; Chain: A, Ribosomal protein L30, ferredoxin-like fold domain 1vq4W01
3I56W 3G6EW 1YJ9W 3CCUW 3J7ZZ 3G71W 3OW2V 1VQOW 1K9MX 1KC8X 1N8RX 4IOCW 3CXCV 1VQNW 5JVGW 4WFBW 3CCEW 3G4SW 1YI2W 1BXYA 1M90X 1NJIX 1M1KX 2ZJRW 2ZJQW 3I55W 1VQ8W 1YJNW 5GAGa 3CCJW 1Q82X 5GADa 1QVGV 1S72W 3PIOW 5JVHW 3CC2W 4IOAW 5DM7W 1YJWW 5HL7W 1K8AX 2ZJPW 5GAHa 1YIJW 4WFAW 3CCLW 2QA4W 1YITW 3CC7W 3DLLW 1KQSV 1K73X 2QEXW 4UY8Z 3CF5W 3CC4W 3CD6W 1VQ7W 1W2BV 1VQ5W 1VQMW 1VQKW 1Q7YX 4WCEW 5GAEa 1YHQW 1VQ6W 1VQPW 3CCVW 4IO9W 4WF9W 1VQ4W 1QVFV 3CPWV 5DM6W 4U67W 3CMAW 1Q81X 2OTLW 4WFNW 2OTJW 3PIPW 3CCQW 3CCSW 1JJ2V 1VQ9W 3CMEW 3CCMW 3CCRW 1KD1X 1Q86X 1VQLW
chains in the Genus database with same CATH superfamily
3I56W 3G6EW 1YJ9W 3CCUW 3J7ZZ 1CTFA 3G71W 4BL2A 3ZG5A 3W7XA 3OW2V 1R6QC 4DKIA 1VQOW 1K9MX 1KC8X 1N8RX 4IOCW 3CXCV 1R6OC 1VQNW 5JVGW 4WFBW 5CA3A 3CCEW 3G4SW 3O2HA 4YKAA 1MG9A 1YI2W 1BXYA 5M19A 3W7WA 5GW7A 1MWSA 1M90X 1NJIX 1M1KX 2ZJRW 2ZJQW 1VQQA 3I55W 1VQ8W 1YJNW 3D3IA 5GAGa 3CCJW 1Q82X 1MWTA 5GADa 3O2OA 1QVGV 4CJNA 1RQSA 1S72W 3PIOW 1DD4A 3CC2W 3DNJA 5JVHW 4IOAW 5DM7W 5M1AA 1YJWW 5HL7W 1K8AX 1RQUA 3O2BA 2ZJPW 1LZWA 5GAHa 4YJMA 1YIJW 4WFAW 1DD3A 3CCLW 1MBXC 1MBUC 3GW1A 2QA4W 1YITW 3CC7W 3DLLW 1KQSV 3W7UA 1K73X 2QEXW 3GQ1A 4UY8Z 3GQ0A 3CF5W 3CC4W 2WA9A 3CD6W 3O1FA 1VQ7W 1W2BV 1VQ5W 1VQMW 1VQKW 1Q7YX 4WCEW 2W9RA 5GAEa 1YHQW 1VQ6W 1VQPW 3CCVW 4CPKA 4BL3A 4IO9W 4YJXA 3W7SA 3ZG0A 4WF9W 1MWRA 1VQ4W 1QVFV 3CPWV 5DM6W 4U67W 3CMAW 1Q81X 2OTLW 4WFNW 1MWUA 2OTJW 4C1NA 1MBVB 3O1FB 3ZFZA 3G3PA 3PIPW 2WA8A 3CCQW 3CCSW 1JJ2V 1VQ9W 1RQVA 3CMEW 3CCMW 3CCRW 3G19A 3W7TA 5M18A 1KD1X 3G1BA 1Q86X 1VQLW
chains in the Genus database with same CATH topology
3I56W 3G6EW 1YJ9W 3CCUW 3J7ZZ 3G71W 3OW2V 1VQOW 1K9MX 1KC8X 1N8RX 4IOCW 3CXCV 1VQNW 5JVGW 4WFBW 3CCEW 3G4SW 1YI2W 1BXYA 1M90X 1NJIX 1M1KX 2ZJRW 2ZJQW 3I55W 1VQ8W 1YJNW 5GAGa 3CCJW 1Q82X 5GADa 1QVGV 1S72W 3PIOW 5JVHW 3CC2W 4IOAW 5DM7W 1YJWW 5HL7W 1K8AX 2ZJPW 5GAHa 1YIJW 4WFAW 3CCLW 2QA4W 1YITW 3CC7W 3DLLW 1KQSV 1K73X 2QEXW 4UY8Z 3CF5W 3CC4W 3CD6W 1VQ7W 1W2BV 1VQ5W 1VQMW 1VQKW 1Q7YX 4WCEW 5GAEa 1YHQW 1VQ6W 1VQPW 3CCVW 4IO9W 4WF9W 1VQ4W 1QVFV 3CPWV 5DM6W 4U67W 3CMAW 1Q81X 2OTLW 4WFNW 2OTJW 4C1NA 3PIPW 3CCQW 3CCSW 1JJ2V 1VQ9W 3CMEW 3CCMW 3CCRW 1KD1X 1Q86X 1VQLW
chains in the Genus database with same CATH homology


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