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


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