1YITH

Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui
Total Genus 36
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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
36
sequence length
171
structure length
160
Chain Sequence
KPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIKVERGEEL
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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 Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance.
pubmed doi rcsb
molecule tags Ribosome/antibiotic
molecule keywords 23S RIBOSOMAL RNA
total genus 36
structure length 160
sequence length 171
ec nomenclature
pdb deposition date 2005-01-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
H PF00252 Ribosomal_L16 Ribosomal protein L16p/L10e
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.1170.10 Alpha Beta Alpha-Beta Complex Aldehyde Oxidoreductase; domain 3 Ribosomal protein L10e/L16 1yitH00
1KQSH 3CCVH 1QVFH 1VQMH 1NJIJ 4IOCJ 5HL7J 5MLCO 1S72H 4WCEJ 3CCSH 5DM6J 3CCJH 3CCQH 3CPWH 1YJ9H 5AN9F 4WFNJ 3CXCH 5GAEN 2OTJH 3PIOJ 2PA2A 3G4SH 1K9MJ 1VQKH 3CCUH 1VQOH 5JVGJ 2ZJRJ 4IOAJ 3CD6H 3CCRH 1YITH 4IO9J 3PIPJ 1Q81J 2QEXH 1VQ5H 2OTLH 4WF9J 3CMEH 1Q7YJ 1VQLH 1N8RJ 1KD1J 5JVHJ 5DM7J 1VQ4H 3CCEH 1Q82J 2ZJQJ 3CC2H 1Q86J 5GADN 5H1SO 1YHQH 1VQPH 3CCLH 1VQ8H 1YJNH 2ZJPJ 3DLLJ 5GAGN 1W2BH 2QA4H 1K73J 1M1KJ 4WFAJ 3CC7H 1VQNH 1YIJH 1M90J 5GAHN 4WFBJ 4UY8M 1KC8J 4U67J 1QVGH 3I55H 3CF5J 3CCMH 1VQ7H 1K8AJ 3G71H 3G6EH 1YI2H 1VQ9H 3J7ZM 3CMAH 3I56H 1WKIA 3OW2H 3CC4H 1JJ2H 1Y69K 1VQ6H 1YJWH
chains in the Genus database with same CATH superfamily
2WK6A 1AZYA 1KQSH 1YTKA 2W3SB 1JROB 3CCVH 1N5WB 1N5XA 4US9A 1QVFH 1FIQC 1FFVB 1N61B 4X46A 1N63B 3C2VA 4GA5A 5AYZA 1VQMH 1NJIJ 1DGJA 3FC4A 4IOCJ 1N62B 1QPQA 3C2EA 5HL7J 3NVZC 1NVJA 1N60B 5MLCO 1FFUB 1QPNA 1NVIE 5HUPA 4WCEJ 1S72H 3CCSH 1QPRA 3SR6C 3B9JC 3TQVA 5DM6J 3GNNA 3CCQH 3CCJH 2B7QA 3C2OA 3C2RA 1YJ9H 3CPWH 3NVWC 1QPOA 4EAFA 5AN9F 4WFNJ 3CXCH 3AM9A 4C7ZA 5GAEN 4YEKA 2OTJH 3PIOJ 3NVVC 1YTEA 2PA2A 3G4SH 1K9MJ 3WNZA 1VQKH 3CCUH 1FO4A 5JVGJ 1VLBA 4GA4A 1VQOH 2DSJA 4C80A 1FM0E 2WK5A 3VMMA 3WO0A 2ZJRJ 3WO1A 3CCRH 3CD6H 4IOAJ 1YITH 4IO9J 5HUOA 3PIPJ 1Q81J 2QEXH 1VQ5H 2OTLH 2WP4A 4I9AA 3ETRC 4WF9J 3CMEH 1Q7YJ 1VQLH 3H5QA 5HULA 1N8RJ 1KD1J 5JVHJ 1SIJA 5DM7J 2W55B 2B7PA 3AN1A 1VQ4H 3BIIE 3CCEH 4EADA 1Q82J 2ZJQJ 3EUB4 4XR5A 3RPFA 3CC2H 1Q86J 5GADN 5H1SO 1YHQH 1VQPH 1JRPB 3CCLH 1VQ8H 1YJNH 2ZJPJ 3DLLJ 5MPOC 2W3RB 5GAGN 2W54B 4YYYA 1W2BH 1VDVA 2JBMA 4LHMA 1OTPA 4C7YA 2QA4H 4US8A 1K73J 2J0FA 1M1KJ 1V97A 3C2FA 4WFAJ 3CC7H 1YIJH 1VQNH 1M90J 3NVYC 5GAHN 1WYGA 2Q5WE 4WFBJ 4UY8M 5AYYA 3L0GA 3NRZC 1KC8J 4U67J 1UOUA 1QVGH 3I55H 2QIEA 3CF5J 3CCMH 1VQ7H 2E3TA 5EP8A 1K8AJ 3G71H 3G6EH 2TPTA 1YI2H 2I14A 3PAJA 4AP8A 1SB3A 5EY3A 1X1OA 4ZOHA 3NS1C 1VQ9H 1QAPA 2B7NA 3J7ZM 4KWVA 3CMAH 3AMZA 2I1OA 4USAA 3I56H 1WKIA 3OW2H 3CC4H 3FAHA 1RM6A 1ZXIB 1JJ2H 1YTDA 1FMAE 2OMDA 1Y69K 3L4PA 1VQ6H 1O4UA 4KWWA 1BRWA 1YJWH 5AYXA 4GA6A
chains in the Genus database with same CATH topology
1KQSH 3CCVH 1QVFH 1VQMH 1NJIJ 4IOCJ 5HL7J 5MLCO 1S72H 4WCEJ 3CCSH 5DM6J 3CCJH 3CCQH 3CPWH 1YJ9H 5AN9F 4WFNJ 3CXCH 5GAEN 2OTJH 3PIOJ 2PA2A 3G4SH 1K9MJ 1VQKH 3CCUH 1VQOH 5JVGJ 2ZJRJ 4IOAJ 3CD6H 3CCRH 1YITH 4IO9J 3PIPJ 1Q81J 2QEXH 1VQ5H 2OTLH 4WF9J 3CMEH 1Q7YJ 1VQLH 1N8RJ 1KD1J 5JVHJ 5DM7J 1VQ4H 3CCEH 1Q82J 2ZJQJ 3CC2H 1Q86J 5GADN 5H1SO 1YHQH 1VQPH 3CCLH 1VQ8H 1YJNH 2ZJPJ 3DLLJ 5GAGN 1W2BH 2QA4H 1K73J 1M1KJ 4WFAJ 3CC7H 1VQNH 1YIJH 1M90J 5GAHN 4WFBJ 4UY8M 1KC8J 4U67J 1QVGH 3I55H 3CF5J 3CCMH 1VQ7H 1K8AJ 3G71H 3G6EH 1YI2H 1VQ9H 3J7ZM 3CMAH 3I56H 1WKIA 3OW2H 3CC4H 1JJ2H 1Y69K 1VQ6H 1YJWH
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1KQS H;  3CCV H;  1QVF H;  1VQM H;  1NJI J;  4IOC J;  5HL7 J;  5MLC O;  1S72 H;  4WCE J;  3CCS H;  5DM6 J;  3CCJ H;  3CCQ H;  3CPW H;  1YJ9 H;  5AN9 F;  4WFN J;  3CXC H;  5GAE N;  2OTJ H;  3PIO J;  2PA2 A;  3G4S H;  1K9M J;  1VQK H;  3CCU H;  1VQO H;  5JVG J;  2ZJR J;  4IOA J;  3CD6 H;  3CCR H;  1YIT H;  4IO9 J;  3PIP J;  1Q81 J;  2QEX H;  1VQ5 H;  2OTL H;  4WF9 J;  3CME H;  1Q7Y J;  1VQL H;  1N8R J;  1KD1 J;  5JVH J;  5DM7 J;  1VQ4 H;  3CCE H;  1Q82 J;  2ZJQ J;  3CC2 H;  1Q86 J;  5GAD N;  5H1S O;  1YHQ H;  1VQP H;  3CCL H;  1VQ8 H;  1YJN H;  2ZJP J;  3DLL J;  5GAG N;  1W2B H;  2QA4 H;  1K73 J;  1M1K J;  4WFA J;  3CC7 H;  1VQN H;  1YIJ H;  1M90 J;  5GAH N;  4WFB J;  4UY8 M;  1KC8 J;  4U67 J;  1QVG H;  3I55 H;  3CF5 J;  3CCM H;  1VQ7 H;  1K8A J;  3G71 H;  3G6E H;  1YI2 H;  1VQ9 H;  3J7Z M;  3CMA H;  3I56 H;  1WKI A;  3OW2 H;  3CC4 H;  1JJ2 H;  1Y69 K;  1VQ6 H;  1YJW H; 
#chains in the Genus database with same CATH topology
 2WK6 A;  1AZY A;  1KQS H;  1YTK A;  2W3S B;  1JRO B;  3CCV H;  1N5W B;  1N5X A;  4US9 A;  1QVF H;  1FIQ C;  1FFV B;  1N61 B;  4X46 A;  1N63 B;  3C2V A;  4GA5 A;  5AYZ A;  1VQM H;  1NJI J;  1DGJ A;  3FC4 A;  4IOC J;  1N62 B;  1QPQ A;  3C2E A;  5HL7 J;  3NVZ C;  1NVJ A;  1N60 B;  5MLC O;  1FFU B;  1QPN A;  1NVI E;  5HUP A;  4WCE J;  1S72 H;  3CCS H;  1QPR A;  3SR6 C;  3B9J C;  3TQV A;  5DM6 J;  3GNN A;  3CCQ H;  3CCJ H;  2B7Q A;  3C2O A;  3C2R A;  1YJ9 H;  3CPW H;  3NVW C;  1QPO A;  4EAF A;  5AN9 F;  4WFN J;  3CXC H;  3AM9 A;  4C7Z A;  5GAE N;  4YEK A;  2OTJ H;  3PIO J;  3NVV C;  1YTE A;  2PA2 A;  3G4S H;  1K9M J;  3WNZ A;  1VQK H;  3CCU H;  1FO4 A;  5JVG J;  1VLB A;  4GA4 A;  1VQO H;  2DSJ A;  4C80 A;  1FM0 E;  2WK5 A;  3VMM A;  3WO0 A;  2ZJR J;  3WO1 A;  3CCR H;  3CD6 H;  4IOA J;  1YIT H;  4IO9 J;  5HUO A;  3PIP J;  1Q81 J;  2QEX H;  1VQ5 H;  2OTL H;  2WP4 A;  4I9A A;  3ETR C;  4WF9 J;  3CME H;  1Q7Y J;  1VQL H;  3H5Q A;  5HUL A;  1N8R J;  1KD1 J;  5JVH J;  1SIJ A;  5DM7 J;  2W55 B;  2B7P A;  3AN1 A;  1VQ4 H;  3BII E;  3CCE H;  4EAD A;  1Q82 J;  2ZJQ J;  3EUB 4;  4XR5 A;  3RPF A;  3CC2 H;  1Q86 J;  5GAD N;  5H1S O;  1YHQ H;  1VQP H;  1JRP B;  3CCL H;  1VQ8 H;  1YJN H;  2ZJP J;  3DLL J;  5MPO C;  2W3R B;  5GAG N;  2W54 B;  4YYY A;  1W2B H;  1VDV A;  2JBM A;  4LHM A;  1OTP A;  4C7Y A;  2QA4 H;  4US8 A;  1K73 J;  2J0F A;  1M1K J;  1V97 A;  3C2F A;  4WFA J;  3CC7 H;  1YIJ H;  1VQN H;  1M90 J;  3NVY C;  5GAH N;  1WYG A;  2Q5W E;  4WFB J;  4UY8 M;  5AYY A;  3L0G A;  3NRZ C;  1KC8 J;  4U67 J;  1UOU A;  1QVG H;  3I55 H;  2QIE A;  3CF5 J;  3CCM H;  1VQ7 H;  2E3T A;  5EP8 A;  1K8A J;  3G71 H;  3G6E H;  2TPT A;  1YI2 H;  2I14 A;  3PAJ A;  4AP8 A;  1SB3 A;  5EY3 A;  1X1O A;  4ZOH A;  3NS1 C;  1VQ9 H;  1QAP A;  2B7N A;  3J7Z M;  4KWV A;  3CMA H;  3AMZ A;  2I1O A;  4USA A;  3I56 H;  1WKI A;  3OW2 H;  3CC4 H;  3FAH A;  1RM6 A;  1ZXI B;  1JJ2 H;  1YTD A;  1FMA E;  2OMD A;  1Y69 K;  3L4P A;  1VQ6 H;  1O4U A;  4KWW A;  1BRW A;  1YJW H;  5AYX A;  4GA6 A; 
#chains in the Genus database with same CATH homology
 1KQS H;  3CCV H;  1QVF H;  1VQM H;  1NJI J;  4IOC J;  5HL7 J;  5MLC O;  1S72 H;  4WCE J;  3CCS H;  5DM6 J;  3CCJ H;  3CCQ H;  3CPW H;  1YJ9 H;  5AN9 F;  4WFN J;  3CXC H;  5GAE N;  2OTJ H;  3PIO J;  2PA2 A;  3G4S H;  1K9M J;  1VQK H;  3CCU H;  1VQO H;  5JVG J;  2ZJR J;  4IOA J;  3CD6 H;  3CCR H;  1YIT H;  4IO9 J;  3PIP J;  1Q81 J;  2QEX H;  1VQ5 H;  2OTL H;  4WF9 J;  3CME H;  1Q7Y J;  1VQL H;  1N8R J;  1KD1 J;  5JVH J;  5DM7 J;  1VQ4 H;  3CCE H;  1Q82 J;  2ZJQ J;  3CC2 H;  1Q86 J;  5GAD N;  5H1S O;  1YHQ H;  1VQP H;  3CCL H;  1VQ8 H;  1YJN H;  2ZJP J;  3DLL J;  5GAG N;  1W2B H;  2QA4 H;  1K73 J;  1M1K J;  4WFA J;  3CC7 H;  1VQN H;  1YIJ H;  1M90 J;  5GAH N;  4WFB J;  4UY8 M;  1KC8 J;  4U67 J;  1QVG H;  3I55 H;  3CF5 J;  3CCM H;  1VQ7 H;  1K8A J;  3G71 H;  3G6E H;  1YI2 H;  1VQ9 H;  3J7Z M;  3CMA H;  3I56 H;  1WKI A;  3OW2 H;  3CC4 H;  1JJ2 H;  1Y69 K;  1VQ6 H;  1YJW H; 
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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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