1VQLH

The structure of the transition state analogue "dcsn" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 40
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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
40
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 40
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 1vqlH00
4IOAJ 2PA2A 3CCRH 1VQ8H 1NJIJ 5MLCO 1YHQH 3I56H 1YI2H 3J7ZM 1K8AJ 1VQ6H 1Q7YJ 3CCEH 3PIPJ 1VQ4H 1QVGH 1YJ9H 1VQ9H 3CMEH 4WFAJ 4IOCJ 1S72H 1K73J 1Y69K 3I55H 1Q86J 3CC4H 3CCMH 4IO9J 1VQLH 5JVHJ 1K9MJ 1KQSH 4WCEJ 3CCVH 3DLLJ 3G6EH 3CCLH 1KC8J 2ZJPJ 1Q81J 3CCUH 4WFBJ 1QVFH 2OTLH 3CC7H 5H1SO 1YJNH 3G71H 3CCSH 5GAGN 1M1KJ 2ZJRJ 5DM6J 1VQMH 4WF9J 1N8RJ 3CXCH 3G4SH 1VQOH 1M90J 1VQ7H 1YIJH 5DM7J 3CC2H 3CD6H 5GAHN 1VQPH 3CCJH 1VQ5H 3CMAH 2QA4H 1KD1J 5JVGJ 1YJWH 5HL7J 1Q82J 1W2BH 4UY8M 2QEXH 1JJ2H 3PIOJ 4WFNJ 3CF5J 1VQNH 2ZJQJ 3CCQH 1YITH 1VQKH 5AN9F 5GADN 3CPWH 1WKIA 4U67J 2OTJH 5GAEN 3OW2H
chains in the Genus database with same CATH superfamily
4IOAJ 1QPNA 2PA2A 3CCRH 3AM9A 1UOUA 3NVVC 2JBMA 1VQ8H 5AYZA 1NJIJ 5MLCO 2B7NA 3OW2H 1VLBA 4US8A 1SIJA 1YHQH 3C2FA 3I56H 1YI2H 3NVYC 3J7ZM 1K8AJ 4GA6A 1QPQA 5HUOA 4C7YA 1VQ6H 1Q7YJ 4KWWA 3CCEH 3PIPJ 1DGJA 3C2VA 1VQ4H 1YTDA 1QVGH 2W3SB 1YJ9H 1VQ9H 4C7ZA 3CMEH 1JROB 4WFAJ 4IOCJ 1V97A 1S72H 1K73J 1Y69K 3I55H 1Q86J 1YTKA 4EADA 2OMDA 1NVIE 1QAPA 3CC4H 3WNZA 4X46A 3EUB4 3CCMH 3L0GA 4IO9J 2I1OA 1VQLH 5JVHJ 1JRPB 1YTEA 3SR6C 1K9MJ 1KQSH 1FFUB 4US9A 4WCEJ 3CCVH 1FMAE 3C2EA 3L4PA 3DLLJ 3G6EH 3CCLH 1KC8J 1FO4A 2ZJPJ 1Q81J 3CCUH 1N5WB 3FC4A 4WFBJ 4YEKA 5AYXA 2I14A 1QVFH 2W54B 5EP8A 1O4UA 3WO0A 2OTLH 2DSJA 5H1SO 3CC7H 2WK5A 3GNNA 1BRWA 1YJNH 3G71H 1X1OA 4EAFA 3CCSH 5GAGN 1AZYA 1M1KJ 1QPRA 5EY3A 3B9JC 5DM6J 2ZJRJ 1VQMH 1RM6A 4WF9J 2E3TA 1FIQC 1N60B 2TPTA 2J0FA 4I9AA 4USAA 1N8RJ 1SB3A 3NRZC 3CXCH 3G4SH 3ETRC 4ZOHA 5AYYA 3AN1A 1VQOH 1N5XA 4GA4A 1M90J 1VQ7H 3NS1C 2W55B 1NVJA 1YIJH 5DM7J 4C80A 3CC2H 3C2OA 3AMZA 3CD6H 5GAHN 1VQPH 1ZXIB 1VQ5H 3CMAH 3CCJH 4YYYA 1FFVB 2QA4H 3NVZC 5JVGJ 1YJWH 1KD1J 5HL7J 3NVWC 1Q82J 2WP4A 3RPFA 2W3RB 1W2BH 4UY8M 4XR5A 5HULA 2Q5WE 5MPOC 2QEXH 3WO1A 1FM0E 1JJ2H 3H5QA 4AP8A 3PIOJ 4WFNJ 3CF5J 1VQNH 3FAHA 3TQVA 4LHMA 3VMMA 2ZJQJ 3CCQH 2B7QA 1WYGA 1VDVA 3PAJA 1YITH 1VQKH 2B7PA 1N63B 3BIIE 1N62B 5AN9F 5GADN 3C2RA 4GA5A 3CPWH 1N61B 1OTPA 2QIEA 1WKIA 4U67J 5HUPA 2OTJH 5GAEN 4KWVA 2WK6A 1QPOA
chains in the Genus database with same CATH topology
4IOAJ 2PA2A 3CCRH 1VQ8H 1NJIJ 5MLCO 1YHQH 3I56H 1YI2H 3J7ZM 1K8AJ 1VQ6H 1Q7YJ 3CCEH 3PIPJ 1VQ4H 1QVGH 1YJ9H 1VQ9H 3CMEH 4WFAJ 4IOCJ 1S72H 1K73J 1Y69K 3I55H 1Q86J 3CC4H 3CCMH 4IO9J 1VQLH 5JVHJ 1K9MJ 1KQSH 4WCEJ 3CCVH 3DLLJ 3G6EH 3CCLH 1KC8J 2ZJPJ 1Q81J 3CCUH 4WFBJ 1QVFH 2OTLH 3CC7H 5H1SO 1YJNH 3G71H 3CCSH 5GAGN 1M1KJ 2ZJRJ 5DM6J 1VQMH 4WF9J 1N8RJ 3CXCH 3G4SH 1VQOH 1M90J 1VQ7H 1YIJH 5DM7J 3CC2H 3CD6H 5GAHN 1VQPH 3CCJH 1VQ5H 3CMAH 2QA4H 1KD1J 5JVGJ 1YJWH 5HL7J 1Q82J 1W2BH 4UY8M 2QEXH 1JJ2H 3PIOJ 4WFNJ 3CF5J 1VQNH 2ZJQJ 3CCQH 1YITH 1VQKH 5AN9F 5GADN 3CPWH 1WKIA 4U67J 2OTJH 5GAEN 3OW2H
chains in the Genus database with same CATH homology


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