1VQ5W

The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 48
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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
48
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 48
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 1vq5W02
3.30.1390.20 Alpha Beta 2-Layer Sandwich Ribosomal Protein L30; Chain: A, Ribosomal protein L30, ferredoxin-like fold domain 1vq5W01
1YHQW 4IOAW 1VQ9W 1VQ6W 1M90X 3CCQW 3CC2W 3CMAW 4WFBW 1KQSV 4IO9W 3G4SW 2ZJRW 4WFAW 5GAGa 2QEXW 1JJ2V 4U67W 5JVHW 3CMEW 5GAHa 2QA4W 3CXCV 1VQ5W 1K9MX 2ZJQW 5HL7W 1VQ4W 4WCEW 1VQOW 1YITW 5JVGW 2OTJW 1YJ9W 1QVFV 5DM6W 3G71W 3CCLW 1YIJW 1KC8X 1VQMW 1VQKW 3CC4W 1W2BV 1BXYA 1Q86X 3PIPW 1VQLW 3CCSW 1YJWW 5GADa 1QVGV 3CCMW 1VQNW 3CCVW 3CCJW 5DM7W 4WF9W 1VQ7W 3CPWV 3G6EW 4IOCW 1K8AX 1Q81X 1N8RX 3CCUW 3CCEW 1Q7YX 5GAEa 1NJIX 3CD6W 3DLLW 3CCRW 2ZJPW 1S72W 1VQPW 4WFNW 4UY8Z 3OW2V 1YI2W 2OTLW 1Q82X 1K73X 1KD1X 1VQ8W 3CC7W 3I55W 3J7ZZ 3I56W 1M1KX 1YJNW 3CF5W 3PIOW
chains in the Genus database with same CATH superfamily
1YHQW 4IOAW 1VQ9W 1VQ6W 3W7TA 1M90X 3CCQW 3W7UA 5M19A 3CC2W 3CMAW 4WFBW 1MBVB 1LZWA 1KQSV 4IO9W 3G4SW 2ZJRW 1MBUC 4WFAW 5GAGa 2QEXW 1JJ2V 1RQSA 3W7XA 4U67W 5JVHW 3CMEW 5GAHa 2QA4W 3O1FB 3CXCV 1VQ5W 1K9MX 2ZJQW 5HL7W 1VQ4W 3G3PA 3O2BA 4WCEW 1VQOW 1YITW 5JVGW 2W9RA 2OTJW 1YJ9W 1QVFV 3W7WA 5DM6W 3G71W 3O1FA 4YJMA 4BL2A 3CCLW 1YIJW 1KC8X 1R6QC 3G1BA 1VQMW 1VQKW 2WA9A 1RQVA 3CC4W 5CA3A 1W2BV 1BXYA 3O2HA 1Q86X 3PIPW 1VQLW 1RQUA 2WA8A 3CCSW 1YJWW 5GADa 1QVGV 3CCMW 1VQNW 5M1AA 3CCVW 1VQQA 3O2OA 4YJXA 3CCJW 3ZG0A 5DM7W 4WF9W 1VQ7W 3GW1A 1MWSA 3CPWV 3G6EW 1MG9A 4IOCW 1K8AX 1Q81X 4DKIA 1DD4A 1MWUA 1DD3A 3ZG5A 1MWTA 1N8RX 3ZFZA 3CCUW 3CCEW 1Q7YX 1MWRA 5GAEa 1NJIX 3CD6W 3DLLW 4CPKA 3CCRW 2ZJPW 1S72W 1VQPW 4WFNW 4UY8Z 5GW7A 1MBXC 1CTFA 3GQ1A 3OW2V 1YI2W 2OTLW 1Q82X 1K73X 1KD1X 1VQ8W 3CC7W 3DNJA 3I55W 1R6OC 3J7ZZ 5M18A 4C1NA 3G19A 4YKAA 3D3IA 3I56W 1M1KX 1YJNW 3W7SA 3CF5W 3GQ0A 3PIOW 4BL3A 4CJNA
chains in the Genus database with same CATH topology
1YHQW 4IOAW 1VQ9W 1VQ6W 1M90X 3CCQW 3CC2W 3CMAW 4WFBW 1KQSV 4IO9W 3G4SW 2ZJRW 4WFAW 5GAGa 2QEXW 1JJ2V 4U67W 5JVHW 3CMEW 5GAHa 2QA4W 3CXCV 1VQ5W 1K9MX 2ZJQW 5HL7W 1VQ4W 4WCEW 1VQOW 1YITW 5JVGW 2OTJW 1YJ9W 1QVFV 5DM6W 3G71W 3CCLW 1YIJW 1KC8X 1VQMW 1VQKW 3CC4W 1W2BV 1BXYA 1Q86X 3PIPW 1VQLW 3CCSW 1YJWW 5GADa 1QVGV 3CCMW 1VQNW 3CCVW 3CCJW 5DM7W 4WF9W 1VQ7W 3CPWV 3G6EW 4IOCW 1K8AX 1Q81X 1N8RX 3CCUW 3CCEW 1Q7YX 5GAEa 1NJIX 3CD6W 3DLLW 3CCRW 2ZJPW 1S72W 1VQPW 4WFNW 4UY8Z 3OW2V 1YI2W 2OTLW 1Q82X 1K73X 1KD1X 1VQ8W 3CC7W 3I55W 3J7ZZ 4C1NA 3I56W 1M1KX 1YJNW 3CF5W 3PIOW
chains in the Genus database with same CATH homology


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