1KD1X

Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui
Total Genus 49

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
49
sequence length
154
structure length
154
Chain Sequence
MHALVQLRGEVNMHTDIQDTLEMLNIHHVNHCTLVPETDAYRGMVAKVNDFVAFGEPSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFALLSEETTLREQGLSPTLRLHPPRGGHDGVKHPVKEGGQLGKHDTEGIDDLLEAMR

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.


  Genus data interpretation
Chord Diagram
EMPTYS1 (2-6)TII2 (28-31)TII1 (10-13)AH1 (15-24)AH2 (39-48)S2 (31-35)S4 (115-117)S3 (52-55)AH3 (59-69)AH6 (143-153)TVIII1 (72-75)AH4 (81-86)AH5 (93-102)TII3 (121-124)3H2 (132-134)TIV2 (127-130)TI1 (48-51)S5 (139-140)3H1 (108-110)Updating...
connected with : NaN
molecule tags Ribosome
publication title The structures of four macrolide antibiotics bound to the large ribosomal subunit.
pubmed doi rcsb
molecule keywords 23S RRNA
total genus 49
structure length 154
sequence length 154
ec nomenclature
pdb deposition date 2001-11-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
X 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 1kd1X02
3.30.1390.20 Alpha Beta 2-Layer Sandwich Ribosomal Protein L30; Chain: A, Ribosomal protein L30, ferredoxin-like fold domain 1kd1X01
3CF5W 1VQ8W 1VQMW 1VQ4W 5GAHa 3I56W 3CCMW 3CCSW 3CCUW 1VQ6W 1VQ5W 1KD1X 1YI2W 1M1KX 2OTLW 3CCQW 3G4SW 2OTJW 1QVFV 5DM6W 1VQNW 1YJNW 3CXCV 4WFBW 4IOCW 4WCEW 3G6EW 4IOAW 3I55W 1M90X 1BXYA 1NJIX 2QEXW 1Q81X 5GADa 3PIPW 2ZJRW 1Q7YX 1VQPW 4WF9W 1YIJW 1KQSV 4WFNW 5JVHW 4WFAW 3G71W 1K8AX 1N8RX 1YJ9W 3PIOW 4IO9W 3CMAW 2ZJPW 3CC4W 1YHQW 1VQ9W 5GAGa 1YITW 3CCLW 3DLLW 3CCEW 5HL7W 3CC7W 3CCVW 1Q86X 3CCJW 1QVGV 1YJWW 1S72W 1JJ2V 3CC2W 5GAEa 1K73X 2ZJQW 3CCRW 3CPWV 1W2BV 1K9MX 5DM7W 3OW2V 1KC8X 3CD6W 1VQLW 1Q82X 4UY8Z 3J7ZZ 3CMEW 1VQ7W 5JVGW 1VQKW 4U67W 2QA4W 1VQOW
chains in the Genus database with same CATH superfamily
5M19A 3CF5W 3W7UA 1VQ8W 1VQMW 1VQ4W 3W7SA 3I56W 5GAHa 1RQSA 3CCMW 3CCSW 3CCUW 2WA9A 1VQ6W 1VQ5W 1KD1X 4YJXA 1RQUA 5GW7A 1YI2W 1M1KX 2OTLW 3CCQW 3G4SW 2OTJW 1QVFV 2WA8A 3ZFZA 5DM6W 5M1AA 5M18A 1VQNW 1YJNW 3CXCV 4WFBW 3DNJA 4IOCW 4BL2A 1LZWA 1DD3A 3D3IA 4WCEW 1DD4A 3G6EW 4IOAW 4DKIA 3I55W 1M90X 1BXYA 4C1NA 4BL3A 1NJIX 2QEXW 1Q81X 5GADa 3PIPW 2ZJRW 1MBXC 1Q7YX 1VQPW 4WF9W 3G3PA 1MWUA 3O2BA 1MBVB 1YIJW 1KQSV 3GW1A 4CJNA 5CA3A 2W9RA 4WFNW 5JVHW 4WFAW 3G71W 1K8AX 1MWSA 1N8RX 1YJ9W 3PIOW 3O2HA 4IO9W 3W7XA 1RQVA 3CMAW 2ZJPW 3CC4W 1YHQW 1VQ9W 4YKAA 1YITW 3CCLW 5GAGa 3ZG0A 3DLLW 3CCEW 5HL7W 3CC7W 3O2OA 1R6OC 3G19A 3CCVW 1Q86X 1MG9A 3CCJW 1CTFA 3O1FA 1QVGV 3W7WA 1YJWW 1S72W 1JJ2V 3CC2W 3G1BA 5GAEa 1K73X 3GQ1A 2ZJQW 3CCRW 3CPWV 3O1FB 1W2BV 3ZG5A 1K9MX 3W7TA 1VQQA 5DM7W 1R6QC 3OW2V 1MBUC 3GQ0A 1KC8X 1MWRA 3CD6W 1VQLW 1Q82X 4CPKA 4UY8Z 3J7ZZ 4YJMA 1MWTA 3CMEW 1VQ7W 5JVGW 1VQKW 4U67W 2QA4W 1VQOW
chains in the Genus database with same CATH topology
3CF5W 1VQ8W 1VQMW 1VQ4W 5GAHa 3I56W 3CCMW 3CCSW 3CCUW 1VQ6W 1VQ5W 1KD1X 1YI2W 1M1KX 2OTLW 3CCQW 3G4SW 2OTJW 1QVFV 5DM6W 1VQNW 1YJNW 3CXCV 4WFBW 4IOCW 4WCEW 3G6EW 4IOAW 3I55W 1M90X 1BXYA 4C1NA 1NJIX 2QEXW 1Q81X 5GADa 3PIPW 2ZJRW 1Q7YX 1VQPW 4WF9W 1YIJW 1KQSV 4WFNW 5JVHW 4WFAW 3G71W 1K8AX 1N8RX 1YJ9W 3PIOW 4IO9W 3CMAW 2ZJPW 3CC4W 1YHQW 1VQ9W 5GAGa 1YITW 3CCLW 3DLLW 3CCEW 5HL7W 3CC7W 3CCVW 1Q86X 3CCJW 1QVGV 1YJWW 1S72W 1JJ2V 3CC2W 5GAEa 1K73X 2ZJQW 3CCRW 3CPWV 1W2BV 1K9MX 5DM7W 3OW2V 1KC8X 3CD6W 1VQLW 1Q82X 4UY8Z 3J7ZZ 3CMEW 1VQ7W 5JVGW 1VQKW 4U67W 2QA4W 1VQOW
chains in the Genus database with same CATH homology

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