1VQ4H

The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 39
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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
39
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 tags Ribosome
molecule keywords 23S ribosomal rna
total genus 39
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 1vq4H00
1S72H 2OTJH 1VQ7H 5HL7J 4IOCJ 1W2BH 4WFBJ 3G6EH 5MLCO 1Q82J 1YI2H 1YITH 1M1KJ 1YHQH 5GAHN 2QEXH 1VQPH 3CC4H 3PIOJ 3CCLH 3CCEH 3CCUH 3CPWH 1KC8J 3G4SH 3CMAH 3CC2H 4UY8M 1KQSH 3CCMH 1Q7YJ 1K8AJ 3OW2H 3I55H 5JVGJ 1VQ4H 4WF9J 1QVFH 1VQ9H 3CF5J 3CXCH 1JJ2H 3CCSH 2OTLH 3CCJH 2QA4H 5AN9F 1YJ9H 4WCEJ 3I56H 1K73J 3PIPJ 1VQNH 4IO9J 1Y69K 3J7ZM 3CC7H 1Q81J 1YIJH 2ZJQJ 1VQ5H 3DLLJ 3CCVH 1VQLH 5H1SO 1YJNH 5DM6J 3CCRH 1VQMH 1WKIA 4U67J 3G71H 5GADN 4IOAJ 1QVGH 2ZJRJ 1YJWH 5GAGN 3CCQH 4WFAJ 3CD6H 2PA2A 1Q86J 1VQ6H 5GAEN 1KD1J 3CMEH 5JVHJ 1N8RJ 5DM7J 1K9MJ 1VQOH 1VQ8H 1NJIJ 1VQKH 4WFNJ 2ZJPJ 1M90J
chains in the Genus database with same CATH superfamily
2W55B 1S72H 4KWVA 3SR6C 3C2OA 4C80A 1WYGA 2OTJH 1VQ7H 1FMAE 5HL7J 4IOCJ 1W2BH 4WFBJ 2OMDA 1ZXIB 5MLCO 3G6EH 1Q82J 1YI2H 1YITH 1M1KJ 1YHQH 5GAHN 2QEXH 1VQPH 3CC4H 1YTEA 3PIOJ 2I14A 3CCLH 3CCEH 3CCUH 4GA6A 1FM0E 1KC8J 3CPWH 3AN1A 5HUPA 3G4SH 1QPRA 3CMAH 4EAFA 3CC2H 4UY8M 1KQSH 3CCMH 1Q7YJ 2DSJA 1N63B 1JRPB 3H5QA 5HUOA 1K8AJ 5HULA 1YTDA 1QAPA 1O4UA 3C2VA 3NS1C 1FFVB 1AZYA 1DGJA 3OW2H 2B7QA 5AYXA 3I55H 2JBMA 5JVGJ 4XR5A 2WK5A 1VQ4H 4WF9J 1QVFH 1FFUB 1VQ9H 3CF5J 1OTPA 3CXCH 1JJ2H 4C7YA 3CCSH 1RM6A 2OTLH 3CCJH 2QA4H 5AN9F 1FO4A 1YJ9H 5MPOC 1YTKA 4WCEJ 3I56H 2I1OA 1QPQA 1NVIE 5EP8A 1K73J 3PIPJ 3FC4A 1N60B 1VQNH 4GA5A 4IO9J 1JROB 2TPTA 1NVJA 3BIIE 4GA4A 2B7NA 4USAA 3PAJA 1Y69K 3J7ZM 4KWWA 2QIEA 3CC7H 1VLBA 1SIJA 1UOUA 1Q81J 3VMMA 3L4PA 2J0FA 1YIJH 3NVZC 2ZJQJ 1VQ5H 5AYYA 4YYYA 3DLLJ 3CCVH 3WO0A 4I9AA 3RPFA 1V97A 1N61B 3ETRC 1VQLH 4EADA 5H1SO 4X46A 1YJNH 2W54B 4US8A 3WO1A 3NVYC 1X1OA 2W3RB 1WKIA 5DM6J 3CCRH 1VQMH 4U67J 3G71H 3NVWC 4LHMA 5GADN 4IOAJ 1QPNA 5AYZA 1QVGH 1N5XA 4YEKA 3L0GA 2ZJRJ 1YJWH 4US9A 2E3TA 3C2FA 5GAGN 3CCQH 1FIQC 3C2RA 4AP8A 1BRWA 1QPOA 4WFAJ 3B9JC 4C7ZA 1N5WB 2WP4A 3CD6H 1N62B 4ZOHA 2PA2A 3AM9A 3TQVA 1Q86J 1VQ6H 5GAEN 1KD1J 3EUB4 3CMEH 1SB3A 3GNNA 3NRZC 3C2EA 5JVHJ 1N8RJ 5DM7J 3AMZA 5EY3A 1VQOH 1K9MJ 2WK6A 1VQ8H 1NJIJ 3NVVC 3WNZA 1VQKH 2Q5WE 2B7PA 4WFNJ 2ZJPJ 1M90J 2W3SB 3FAHA 1VDVA
chains in the Genus database with same CATH topology
1S72H 2OTJH 1VQ7H 5HL7J 4IOCJ 1W2BH 4WFBJ 3G6EH 5MLCO 1Q82J 1YI2H 1YITH 1M1KJ 1YHQH 5GAHN 2QEXH 1VQPH 3CC4H 3PIOJ 3CCLH 3CCEH 3CCUH 3CPWH 1KC8J 3G4SH 3CMAH 3CC2H 4UY8M 1KQSH 3CCMH 1Q7YJ 1K8AJ 3OW2H 3I55H 5JVGJ 1VQ4H 4WF9J 1QVFH 1VQ9H 3CF5J 3CXCH 1JJ2H 3CCSH 2OTLH 3CCJH 2QA4H 5AN9F 1YJ9H 4WCEJ 3I56H 1K73J 3PIPJ 1VQNH 4IO9J 1Y69K 3J7ZM 3CC7H 1Q81J 1YIJH 2ZJQJ 1VQ5H 3DLLJ 3CCVH 1VQLH 5H1SO 1YJNH 5DM6J 3CCRH 1VQMH 1WKIA 4U67J 3G71H 5GADN 4IOAJ 1QVGH 2ZJRJ 1YJWH 5GAGN 3CCQH 4WFAJ 3CD6H 2PA2A 1Q86J 1VQ6H 5GAEN 1KD1J 3CMEH 5JVHJ 1N8RJ 5DM7J 1K9MJ 1VQOH 1VQ8H 1NJIJ 1VQKH 4WFNJ 2ZJPJ 1M90J
chains in the Genus database with same CATH homology


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