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


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