1VQPH

The structure of the transition state analogue "rap" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 41
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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
41
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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molecule tags Ribosome
molecule keywords 23S ribosomal rna
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
total genus 41
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 1vqpH00
1VQNH 2QA4H 1NJIJ 1KD1J 5GADN 1VQKH 5JVGJ 4IOAJ 1M90J 2ZJPJ 4IOCJ 3PIPJ 4IO9J 3I55H 1K8AJ 4WF9J 1S72H 3CCJH 3CCSH 1YIJH 1VQLH 4WCEJ 4UY8M 1Q82J 3CPWH 3CCVH 1Y69K 3CF5J 1VQOH 1VQ5H 3G6EH 1M1KJ 1K9MJ 1KQSH 3CXCH 3CCLH 3PIOJ 1YJWH 1YJ9H 3CC4H 2PA2A 1VQ4H 3CMAH 3G71H 1QVGH 1QVFH 1VQMH 1YJNH 1JJ2H 1Q7YJ 2ZJQJ 2OTJH 3CMEH 1VQ7H 3CCUH 2QEXH 1WKIA 3CCMH 3I56H 1Q86J 3CC7H 3DLLJ 5DM6J 4WFBJ 4WFNJ 3CCRH 1VQ8H 3G4SH 1VQ9H 5GAHN 2OTLH 1N8RJ 1YI2H 1YHQH 3CD6H 2ZJRJ 5JVHJ 5HL7J 1VQPH 1YITH 1VQ6H 5GAEN 5MLCO 1K73J 3CCQH 4WFAJ 3OW2H 3CC2H 5AN9F 1KC8J 5H1SO 5DM7J 5GAGN 3J7ZM 4U67J 3CCEH 1Q81J 1W2BH
chains in the Genus database with same CATH superfamily
3C2FA 4C7YA 2QA4H 1VQNH 1NJIJ 1KD1J 5GADN 2B7QA 3L4PA 1N63B 1N5XA 2B7PA 4GA6A 4YYYA 1VQKH 1SIJA 3AM9A 2JBMA 5JVGJ 4USAA 5AYYA 3H5QA 2W3SB 4IOAJ 1M90J 1NVIE 1QPQA 3RPFA 1RM6A 2I14A 3BIIE 2ZJPJ 4IOCJ 5MPOC 3PIPJ 4I9AA 2W54B 1QAPA 4XR5A 4IO9J 3I55H 1K8AJ 4WF9J 1S72H 3CCJH 3CCSH 1YIJH 1VQLH 3C2VA 3WO0A 3NVYC 4WCEJ 1FO4A 4UY8M 1ZXIB 2W55B 1FFUB 1Q82J 3CPWH 1JRPB 3NVWC 3CCVH 1Y69K 4ZOHA 1SB3A 3CF5J 1VQOH 2TPTA 4EAFA 1VDVA 1VQ5H 4LHMA 3G6EH 1M1KJ 3AN1A 1K9MJ 1KQSH 3CXCH 3PAJA 3CCLH 3PIOJ 1YJWH 4C7ZA 1YJ9H 3FAHA 2PA2A 4EADA 3CC4H 5AYZA 1VQ4H 5EY3A 3AMZA 1O4UA 3CMAH 2E3TA 3G71H 1QVGH 4AP8A 1QVFH 1UOUA 1VQMH 3NVVC 1YJNH 3VMMA 1JJ2H 1Q7YJ 5EP8A 5AYXA 4C80A 2ZJQJ 1JROB 2OTJH 3B9JC 3ETRC 3C2EA 1W2BH 1DGJA 3CMEH 2QIEA 1N60B 3TQVA 1YTKA 4KWVA 1VQ7H 2WK5A 3CCUH 2QEXH 1WKIA 5HULA 3CCMH 3I56H 3L0GA 1Q86J 2I1OA 3CC7H 3DLLJ 1YTEA 1V97A 5DM6J 1OTPA 4US8A 4WFBJ 4WFNJ 1N62B 3WNZA 1FMAE 2B7NA 3CCRH 1VQ8H 3WO1A 1FFVB 1QPOA 3G4SH 3C2OA 4US9A 1VQ9H 4GA4A 3NS1C 1BRWA 1N61B 5HUPA 2DSJA 5GAHN 2OTLH 4X46A 3NRZC 1N8RJ 1YI2H 1YHQH 3CD6H 1YTDA 4YEKA 1VLBA 2OMDA 2ZJRJ 5JVHJ 1X1OA 5HL7J 1VQPH 1YITH 1VQ6H 5GAEN 5MLCO 1K73J 1FM0E 2WK6A 1QPRA 3CCQH 4WFAJ 3C2RA 3NVZC 1AZYA 4GA5A 2J0FA 3GNNA 3SR6C 3OW2H 3CC2H 3FC4A 5AN9F 4KWWA 2Q5WE 1QPNA 1KC8J 1WYGA 5HUOA 5H1SO 5DM7J 5GAGN 3J7ZM 4U67J 3EUB4 2W3RB 3CCEH 1Q81J 1FIQC 1N5WB 2WP4A 1NVJA
chains in the Genus database with same CATH topology
1VQNH 2QA4H 1NJIJ 1KD1J 5GADN 1VQKH 5JVGJ 4IOAJ 1M90J 2ZJPJ 4IOCJ 3PIPJ 4IO9J 3I55H 1K8AJ 4WF9J 1S72H 3CCJH 3CCSH 1YIJH 1VQLH 4WCEJ 4UY8M 1Q82J 3CPWH 3CCVH 1Y69K 3CF5J 1VQOH 1VQ5H 3G6EH 1M1KJ 1K9MJ 1KQSH 3CXCH 3CCLH 3PIOJ 1YJWH 1YJ9H 3CC4H 2PA2A 1VQ4H 3CMAH 3G71H 1QVGH 1QVFH 1VQMH 1YJNH 1JJ2H 1Q7YJ 2ZJQJ 2OTJH 3CMEH 1VQ7H 3CCUH 2QEXH 1WKIA 3CCMH 3I56H 1Q86J 3CC7H 3DLLJ 5DM6J 4WFBJ 4WFNJ 3CCRH 1VQ8H 3G4SH 1VQ9H 5GAHN 2OTLH 1N8RJ 1YI2H 1YHQH 3CD6H 2ZJRJ 5JVHJ 5HL7J 1VQPH 1YITH 1VQ6H 5GAEN 5MLCO 1K73J 3CCQH 4WFAJ 3OW2H 3CC2H 5AN9F 1KC8J 5H1SO 5DM7J 5GAGN 3J7ZM 4U67J 3CCEH 1Q81J 1W2BH
chains in the Genus database with same CATH homology


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