1VQ5H

The structure of the transition state analogue "raa" 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 1vq5H00
1VQNH 1Q82J 2ZJRJ 4UY8M 3CC2H 1VQPH 2ZJQJ 1QVFH 3CCSH 5GADN 3PIPJ 1YITH 1YJNH 1VQKH 5GAGN 1VQ8H 1VQ4H 3OW2H 1YJ9H 5JVHJ 1YJWH 1Q7YJ 4IO9J 1JJ2H 5GAHN 1Q86J 2PA2A 3I55H 3G4SH 2ZJPJ 3CC4H 1VQ9H 3CCMH 3CPWH 4WFBJ 1VQOH 2QEXH 3I56H 1KD1J 1VQLH 1Q81J 5DM7J 1WKIA 2OTJH 3PIOJ 3DLLJ 4WFAJ 3CXCH 1W2BH 3CCJH 5JVGJ 1K73J 1S72H 1Y69K 1VQMH 3CMEH 3CCQH 3CC7H 1VQ5H 4WFNJ 1K9MJ 1K8AJ 3CF5J 3CCVH 1M1KJ 4U67J 5MLCO 2QA4H 1VQ7H 1M90J 5DM6J 3CCRH 1YI2H 1NJIJ 1QVGH 1KC8J 3CCLH 4WF9J 1YHQH 4WCEJ 5GAEN 3CMAH 1VQ6H 3CD6H 3J7ZM 4IOCJ 3CCEH 5AN9F 3G71H 1YIJH 1N8RJ 1KQSH 5H1SO 4IOAJ 3CCUH 3G6EH 5HL7J 2OTLH
chains in the Genus database with same CATH superfamily
4GA4A 3C2VA 3TQVA 1VQNH 1Q82J 3NVWC 2ZJRJ 4LHMA 2B7QA 4UY8M 2B7PA 2JBMA 3CC2H 1JROB 1QPRA 1VDVA 1SB3A 1VQPH 3WO0A 3L0GA 2B7NA 2ZJQJ 3AM9A 1QVFH 1O4UA 1YTEA 1QAPA 1AZYA 5GADN 3CCSH 1YTDA 3H5QA 3PIPJ 4C80A 5EY3A 4X46A 1ZXIB 5HUPA 1FMAE 3L4PA 1YITH 1YJNH 1FO4A 1VQKH 5GAGN 4USAA 1FM0E 1FIQC 1VQ8H 1VQ4H 3OW2H 3FC4A 1VLBA 2W55B 1YJ9H 5JVHJ 3WO1A 1YJWH 1Q7YJ 4EAFA 4IO9J 1JJ2H 4GA6A 4AP8A 4EADA 3C2RA 5GAHN 1N62B 4I9AA 1Q86J 2PA2A 2WK5A 3SR6C 3I55H 3G4SH 5AYYA 2ZJPJ 3AMZA 3C2FA 3AN1A 5HULA 4US8A 1FFVB 1N63B 4GA5A 4YEKA 3CC4H 1VQ9H 3CCMH 3GNNA 3RPFA 3CPWH 4WFBJ 1N60B 1X1OA 1VQOH 2QEXH 3I56H 1KD1J 3NS1C 1FFUB 1VQLH 2J0FA 1Q81J 5DM7J 1WKIA 3BIIE 2E3TA 2WP4A 4C7ZA 2OTJH 3PIOJ 3DLLJ 4WFAJ 3CXCH 1WYGA 3NVVC 3C2EA 5AYXA 4C7YA 1NVIE 1YTKA 1W2BH 5HUOA 3CCJH 5JVGJ 1K73J 1S72H 3NVZC 2W3RB 1Y69K 4YYYA 1VQMH 3PAJA 1JRPB 1N61B 2OMDA 1QPQA 2WK6A 2W3SB 3CCQH 3CMEH 3CC7H 2I1OA 1BRWA 1VQ5H 4WFNJ 1K9MJ 1K8AJ 3CF5J 3CCVH 1NVJA 5AYZA 1QPNA 2QIEA 1M1KJ 2I14A 4U67J 1N5XA 5MLCO 1DGJA 2QA4H 1VQ7H 1RM6A 2Q5WE 3C2OA 2W54B 5DM6J 1M90J 5MPOC 3B9JC 3CCRH 1YI2H 1NJIJ 1QVGH 1KC8J 1OTPA 3NRZC 3CCLH 3VMMA 4WF9J 1YHQH 1N5WB 5EP8A 2DSJA 5GAEN 4WCEJ 4KWVA 3WNZA 3CMAH 1VQ6H 3CD6H 3J7ZM 4IOCJ 3CCEH 2TPTA 4ZOHA 4XR5A 5AN9F 1SIJA 4KWWA 1QPOA 1V97A 1UOUA 3EUB4 3G71H 1YIJH 1N8RJ 1KQSH 3NVYC 5H1SO 4IOAJ 3CCUH 3G6EH 5HL7J 2OTLH 4US9A 3ETRC 3FAHA
chains in the Genus database with same CATH topology
1VQNH 1Q82J 2ZJRJ 4UY8M 3CC2H 1VQPH 2ZJQJ 1QVFH 3CCSH 5GADN 3PIPJ 1YITH 1YJNH 1VQKH 5GAGN 1VQ8H 1VQ4H 3OW2H 1YJ9H 5JVHJ 1YJWH 1Q7YJ 4IO9J 1JJ2H 5GAHN 1Q86J 2PA2A 3I55H 3G4SH 2ZJPJ 3CC4H 1VQ9H 3CCMH 3CPWH 4WFBJ 1VQOH 2QEXH 3I56H 1KD1J 1VQLH 1Q81J 5DM7J 1WKIA 2OTJH 3PIOJ 3DLLJ 4WFAJ 3CXCH 1W2BH 3CCJH 5JVGJ 1K73J 1S72H 1Y69K 1VQMH 3CMEH 3CCQH 3CC7H 1VQ5H 4WFNJ 1K9MJ 1K8AJ 3CF5J 3CCVH 1M1KJ 4U67J 5MLCO 2QA4H 1VQ7H 1M90J 5DM6J 3CCRH 1YI2H 1NJIJ 1QVGH 1KC8J 3CCLH 4WF9J 1YHQH 4WCEJ 5GAEN 3CMAH 1VQ6H 3CD6H 3J7ZM 4IOCJ 3CCEH 5AN9F 3G71H 1YIJH 1N8RJ 1KQSH 5H1SO 4IOAJ 3CCUH 3G6EH 5HL7J 2OTLH
chains in the Genus database with same CATH homology


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