1VQPW

The structure of the transition state analogue "rap" 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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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 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 1vqpW02
3.30.1390.20 Alpha Beta 2-Layer Sandwich Ribosomal Protein L30; Chain: A, Ribosomal protein L30, ferredoxin-like fold domain 1vqpW01
5JVGW 3CCMW 3CXCV 1BXYA 1Q81X 1YJNW 5GAHa 3G4SW 1YHQW 4WF9W 4WFBW 3CCQW 1VQKW 1YIJW 1KQSV 3I56W 1Q82X 5JVHW 3J7ZZ 3G6EW 1Q7YX 3DLLW 4WFAW 1VQ9W 1YI2W 3CC2W 1VQOW 4UY8Z 1YJWW 1Q86X 1VQMW 2ZJRW 3CCEW 1VQNW 1K73X 1QVFV 1VQ4W 3CC7W 1VQ8W 4IOCW 1VQ6W 3CC4W 3CPWV 2OTJW 5HL7W 1QVGV 5GADa 4IO9W 1K8AX 3CCVW 4U67W 1N8RX 3G71W 3CMEW 1KC8X 3PIPW 1YJ9W 1M1KX 1K9MX 3PIOW 3CCUW 4IOAW 1VQ7W 4WCEW 1JJ2V 1YITW 1NJIX 5GAGa 3CMAW 1VQLW 2QA4W 1KD1X 3CD6W 1W2BV 3OW2V 1VQ5W 1S72W 3CCRW 3I55W 1VQPW 5GAEa 2OTLW 2ZJPW 2QEXW 1M90X 3CF5W 4WFNW 3CCJW 5DM7W 5DM6W 2ZJQW 3CCLW 3CCSW
chains in the Genus database with same CATH superfamily
5JVGW 4CJNA 5M19A 2W9RA 3CCMW 3CXCV 3O2BA 1BXYA 1MWTA 3W7SA 1Q81X 1YJNW 1MBXC 5GAHa 3G3PA 5GW7A 5M1AA 3G4SW 1YHQW 4BL3A 4WF9W 4WFBW 1CTFA 3CCQW 1VQKW 1LZWA 3W7TA 1YIJW 1KQSV 3I56W 1MBVB 1Q82X 1RQUA 5JVHW 2WA8A 4C1NA 3J7ZZ 3G6EW 1Q7YX 5CA3A 1MWRA 3ZG5A 4BL2A 3DLLW 4WFAW 1VQ9W 1YI2W 3CC2W 3O1FA 4YJMA 1VQOW 4UY8Z 4CPKA 1YJWW 1Q86X 1VQMW 2ZJRW 3CCEW 3W7XA 1VQNW 1K73X 1QVFV 1VQ4W 3O2OA 3ZFZA 3CC7W 1VQ8W 4IOCW 3GW1A 1RQSA 1VQ6W 3CC4W 3CPWV 2OTJW 1RQVA 5HL7W 1QVGV 3ZG0A 5GADa 4IO9W 1K8AX 3CCVW 4U67W 1N8RX 3O1FB 1MG9A 3G71W 3G1BA 5M18A 3CMEW 1KC8X 3PIPW 1YJ9W 3DNJA 1M1KX 3O2HA 1K9MX 3PIOW 3CCUW 4IOAW 1VQ7W 4WCEW 4YJXA 1JJ2V 1YITW 1NJIX 3GQ0A 5GAGa 1R6QC 3GQ1A 3CMAW 1VQLW 3W7WA 2WA9A 1MWUA 2QA4W 1KD1X 1R6OC 3CD6W 1DD4A 1W2BV 3OW2V 1VQ5W 1S72W 3CCRW 3D3IA 4DKIA 3I55W 1VQPW 5GAEa 2OTLW 2ZJPW 4YKAA 3W7UA 1VQQA 2QEXW 1M90X 3CF5W 1MBUC 4WFNW 3CCJW 3G19A 5DM7W 5DM6W 2ZJQW 1DD3A 3CCLW 3CCSW 1MWSA
chains in the Genus database with same CATH topology
5JVGW 3CCMW 3CXCV 1BXYA 1Q81X 1YJNW 5GAHa 3G4SW 1YHQW 4WF9W 4WFBW 3CCQW 1VQKW 1YIJW 1KQSV 3I56W 1Q82X 5JVHW 4C1NA 3J7ZZ 3G6EW 1Q7YX 3DLLW 4WFAW 1VQ9W 1YI2W 3CC2W 1VQOW 4UY8Z 1YJWW 1Q86X 1VQMW 2ZJRW 3CCEW 1VQNW 1K73X 1QVFV 1VQ4W 3CC7W 1VQ8W 4IOCW 1VQ6W 3CC4W 3CPWV 2OTJW 5HL7W 1QVGV 5GADa 4IO9W 1K8AX 3CCVW 4U67W 1N8RX 3G71W 3CMEW 1KC8X 3PIPW 1YJ9W 1M1KX 1K9MX 3PIOW 3CCUW 4IOAW 1VQ7W 4WCEW 1JJ2V 1YITW 1NJIX 5GAGa 3CMAW 1VQLW 2QA4W 1KD1X 3CD6W 1W2BV 3OW2V 1VQ5W 1S72W 3CCRW 3I55W 1VQPW 5GAEa 2OTLW 2ZJPW 2QEXW 1M90X 3CF5W 4WFNW 3CCJW 5DM7W 5DM6W 2ZJQW 3CCLW 3CCSW
chains in the Genus database with same CATH homology


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