1VQMH

The structure of the transition state analogue "dan" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 37
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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
37
sequence length
171
structure length
160
Chain Sequence
KPASMYRDIDKPAYTRREYITGIPGSKIAQHKMGRKQKDADDYPVQISLIVEETVQLRHGSLEASRLSANRHLIKELGEEGDYKMTLRKFPHQVLRENKDGMRAAFGKIVGTAARVQAGEQLFTAYCNVEDAEHVKEAFRRAYNKITPSCRIDSSPAGNA
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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 keywords 23S ribosomal rna
molecule tags Ribosome
total genus 37
structure length 160
sequence length 171
ec nomenclature
pdb deposition date 2004-12-16
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 1vqmH00
3CCLH 1YHQH 1VQOH 3CC7H 1VQPH 3CXCH 1JJ2H 1Y69K 3DLLJ 1KC8J 1Q7YJ 4IOCJ 2ZJQJ 3PIPJ 2ZJRJ 3G6EH 1VQ6H 5HL7J 4WF9J 1YITH 3J7ZM 1K8AJ 1Q81J 2QEXH 1M1KJ 3PIOJ 3CC2H 4WFNJ 5DM6J 5GAHN 3CMAH 5GAGN 3CCVH 1Q86J 2PA2A 3CCMH 1QVFH 1N8RJ 1VQ4H 5JVHJ 1W2BH 1QVGH 1NJIJ 1YIJH 1K73J 1KQSH 3CMEH 2QA4H 1S72H 3G71H 1YJWH 3CC4H 3OW2H 1VQ8H 5AN9F 5GAEN 5JVGJ 1VQMH 2OTLH 4IO9J 1YJNH 1VQLH 1VQ9H 3I55H 2OTJH 4IOAJ 1K9MJ 1M90J 1Q82J 3CPWH 3CCJH 4UY8M 1VQ5H 3CF5J 4WFBJ 1WKIA 5GADN 4WFAJ 1KD1J 5H1SO 3CCRH 5DM7J 3CCUH 3CCEH 3CD6H 2ZJPJ 5MLCO 3CCSH 4U67J 3CCQH 1YJ9H 1YI2H 3G4SH 3I56H 1VQKH 1VQ7H 4WCEJ 1VQNH
chains in the Genus database with same CATH superfamily
3CCLH 1YHQH 1VQOH 3TQVA 1AZYA 1VQPH 3CC7H 3CXCH 2TPTA 2J0FA 1JJ2H 1Y69K 3DLLJ 1KC8J 1Q7YJ 1QPQA 5AYYA 1QPRA 4IOCJ 3L0GA 5HUPA 3PIPJ 2OMDA 2ZJQJ 2ZJRJ 3AN1A 3H5QA 2QIEA 1QPNA 1OTPA 3G6EH 1YTEA 1N5WB 4EAFA 1VQ6H 5HL7J 4WF9J 4KWVA 1YITH 3C2OA 3PAJA 3C2VA 4USAA 3J7ZM 1K8AJ 5EY3A 4GA5A 1N60B 1Q81J 3RPFA 1FM0E 2QEXH 1M1KJ 4ZOHA 4AP8A 3PIOJ 5MPOC 3CC2H 2B7NA 4WFNJ 2WK6A 5DM6J 5GAHN 3L4PA 5GAGN 3CMAH 3CCVH 1Q86J 1VDVA 2PA2A 3SR6C 3CCMH 2W3SB 1QVFH 1N8RJ 1VQ4H 5JVHJ 2B7PA 1SIJA 4XR5A 1WYGA 1W2BH 4EADA 1QVGH 1NJIJ 1YIJH 4C80A 1N5XA 1V97A 3NVZC 1K73J 1KQSH 2E3TA 2I14A 3NS1C 5EP8A 3CMEH 2QA4H 3WNZA 4YYYA 1S72H 3G71H 5AYXA 1YJWH 3WO0A 3CC4H 3NRZC 3OW2H 4US8A 1VQ8H 3C2RA 5AN9F 5GAEN 1FFVB 1X1OA 5JVGJ 1FMAE 4X46A 1VQMH 2OTLH 1QPOA 4KWWA 4IO9J 4C7YA 1SB3A 4YEKA 1YJNH 3ETRC 1FFUB 1ZXIB 4GA6A 1VQ9H 1VQLH 3I55H 2OTJH 4IOAJ 1K9MJ 3NVVC 2W54B 2B7QA 1M90J 3B9JC 3WO1A 2W3RB 3FC4A 1Q82J 1YTDA 3CPWH 3C2EA 3NVYC 3AM9A 3EUB4 3NVWC 3CCJH 4UY8M 1VLBA 1VQ5H 5HULA 3CF5J 4WFBJ 1WKIA 2WK5A 1FIQC 2DSJA 1BRWA 2I1OA 1NVIE 4C7ZA 5GADN 4WFAJ 3GNNA 1KD1J 3AMZA 5H1SO 3CCRH 1QAPA 4GA4A 4LHMA 5DM7J 3CCUH 4I9AA 3CCEH 3CD6H 1RM6A 1O4UA 2ZJPJ 3FAHA 5MLCO 3CCSH 3BIIE 4U67J 1N62B 2JBMA 1N63B 4US9A 1YTKA 3CCQH 1UOUA 5AYZA 5HUOA 1FO4A 1YJ9H 2W55B 2Q5WE 1JRPB 3C2FA 1YI2H 1DGJA 3G4SH 3I56H 1N61B 1VQKH 1JROB 2WP4A 1VQ7H 4WCEJ 1NVJA 3VMMA 1VQNH
chains in the Genus database with same CATH topology
3CCLH 1YHQH 1VQOH 3CC7H 1VQPH 3CXCH 1JJ2H 1Y69K 3DLLJ 1KC8J 1Q7YJ 4IOCJ 2ZJQJ 3PIPJ 2ZJRJ 3G6EH 1VQ6H 5HL7J 4WF9J 1YITH 3J7ZM 1K8AJ 1Q81J 2QEXH 1M1KJ 3PIOJ 3CC2H 4WFNJ 5DM6J 5GAHN 3CMAH 5GAGN 3CCVH 1Q86J 2PA2A 3CCMH 1QVFH 1N8RJ 1VQ4H 5JVHJ 1W2BH 1QVGH 1NJIJ 1YIJH 1K73J 1KQSH 3CMEH 2QA4H 1S72H 3G71H 1YJWH 3CC4H 3OW2H 1VQ8H 5AN9F 5GAEN 5JVGJ 1VQMH 2OTLH 4IO9J 1YJNH 1VQLH 1VQ9H 3I55H 2OTJH 4IOAJ 1K9MJ 1M90J 1Q82J 3CPWH 3CCJH 4UY8M 1VQ5H 3CF5J 4WFBJ 1WKIA 5GADN 4WFAJ 1KD1J 5H1SO 3CCRH 5DM7J 3CCUH 3CCEH 3CD6H 2ZJPJ 5MLCO 3CCSH 4U67J 3CCQH 1YJ9H 1YI2H 3G4SH 3I56H 1VQKH 1VQ7H 4WCEJ 1VQNH
chains in the Genus database with same CATH homology


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