1VQ4H

The structure of the transition state analogue "daa" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 39
204060801001201400510152025303540
Genus TraceResidueGenus

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

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
EMPTYS3 (55-58)TIV4 (113-116)S4 (83-87)S1 (32-34)TI1 (35-38)TIV1 (33-36)TIV2 (78-81)3H3 (40-42)TIV3 (111-114)AH1 (59-77)AH2 (142-154)TII1 (128-131)O1 (90-92)S6 (119-127)S7 (131-138)3H2 (17-19)S2 (45-51)TI3 (154-157)S5 (93-97)3H1 (3-5)TI2 (139-142)Updating...
connected with : NaN
molecule tags Ribosome
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
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
1YJWH 1S72H 3CCEH 5DM7J 5HL7J 3CXCH 5MLCO 1VQ7H 3CC7H 1KD1J 3G71H 1Q86J 1QVFH 1VQLH 3CF5J 3PIOJ 1VQ6H 1K9MJ 3CD6H 1YHQH 3CCQH 2QEXH 1NJIJ 1Q7YJ 1M90J 3CMEH 1KQSH 1YI2H 3G6EH 1VQ4H 3CCVH 1VQ8H 4IOCJ 4UY8M 1W2BH 1K8AJ 1WKIA 1YITH 5GADN 3I55H 2ZJPJ 2QA4H 5GAHN 4WFAJ 3CMAH 3OW2H 4IOAJ 4IO9J 1Q81J 2OTLH 4WFBJ 1Y69K 3CC2H 1YJ9H 4WFNJ 5JVGJ 3CCRH 3CC4H 1VQOH 3J7ZM 5H1SO 4U67J 1K73J 3CCUH 3I56H 2OTJH 1Q82J 1YIJH 3CCJH 1M1KJ 1VQNH 5GAGN 1VQ5H 3G4SH 4WF9J 2ZJQJ 5AN9F 3CCSH 1VQPH 3PIPJ 5DM6J 1N8RJ 3CCMH 1YJNH 3DLLJ 2PA2A 5JVHJ 1QVGH 1VQMH 4WCEJ 1VQ9H 3CCLH 5GAEN 2ZJRJ 3CPWH 1KC8J 1VQKH 1JJ2H
chains in the Genus database with same CATH superfamily
1YJWH 1S72H 3VMMA 4GA4A 4ZOHA 3NVZC 3CCEH 5DM7J 5HL7J 3CXCH 5MLCO 2WK5A 1OTPA 1VQ7H 2WK6A 4AP8A 3CC7H 1KD1J 3G71H 1Q86J 2W3RB 1QVFH 3AN1A 1VQLH 3WO1A 3CF5J 3NVWC 1VDVA 3TQVA 1RM6A 1N62B 3PIOJ 1JROB 2I1OA 3BIIE 3NVVC 1VQ6H 1QPRA 1QPNA 2W55B 3WO0A 1K9MJ 3CD6H 1YHQH 1WYGA 2QEXH 2I14A 3CCQH 1QPOA 3WNZA 1NJIJ 1Q7YJ 1M90J 3CMEH 2B7NA 1KQSH 1NVIE 1VLBA 1YI2H 3G6EH 3RPFA 1JRPB 3FC4A 1VQ4H 3CCVH 1QPQA 1FM0E 3ETRC 1VQ8H 4IOCJ 1N5XA 4UY8M 1W2BH 1FFUB 1K8AJ 1WKIA 1YITH 1YTEA 5GADN 3I55H 2ZJPJ 2QA4H 3SR6C 5HULA 5GAHN 3AMZA 2Q5WE 4EAFA 3NRZC 4WFAJ 3CMAH 2DSJA 3OW2H 3C2RA 1FMAE 4X46A 3C2EA 1YTDA 4GA6A 4IOAJ 5HUOA 5AYZA 5HUPA 4IO9J 1Q81J 2OTLH 1QAPA 4WFBJ 1NVJA 3C2OA 1Y69K 5MPOC 3CC2H 1YJ9H 4WFNJ 1DGJA 5JVGJ 3CCRH 1FIQC 3CC4H 4C7YA 2OMDA 1VQOH 3J7ZM 1O4UA 3H5QA 5H1SO 4U67J 1K73J 4KWWA 4YYYA 1N60B 1UOUA 4KWVA 2W3SB 4GA5A 3CCUH 3I56H 1YTKA 2E3TA 2OTJH 1Q82J 1SB3A 3NVYC 1YIJH 5EP8A 3CCJH 1FFVB 3PAJA 2TPTA 1N63B 4C80A 1M1KJ 1VQNH 1ZXIB 3B9JC 5GAGN 5AYXA 2B7PA 1VQ5H 3G4SH 4WF9J 3NS1C 4US9A 2ZJQJ 5AN9F 3CCSH 1VQPH 4XR5A 4US8A 1JJ2H 3PIPJ 4EADA 5DM6J 1N8RJ 3C2VA 1BRWA 3CCMH 2QIEA 4LHMA 1YJNH 1N61B 3DLLJ 1V97A 3GNNA 1N5WB 2PA2A 5JVHJ 1QVGH 1VQMH 1SIJA 1AZYA 4WCEJ 3AM9A 1VQ9H 1FO4A 5EY3A 5GAEN 3CCLH 4YEKA 3EUB4 4I9AA 2J0FA 2W54B 2ZJRJ 5AYYA 4C7ZA 2JBMA 3CPWH 2B7QA 3FAHA 3L0GA 1KC8J 2WP4A 4USAA 1VQKH 3L4PA 1X1OA 3C2FA
chains in the Genus database with same CATH topology
1YJWH 1S72H 3CCEH 5DM7J 5HL7J 3CXCH 5MLCO 1VQ7H 3CC7H 1KD1J 3G71H 1Q86J 1QVFH 1VQLH 3CF5J 3PIOJ 1VQ6H 1K9MJ 3CD6H 1YHQH 3CCQH 2QEXH 1NJIJ 1Q7YJ 1M90J 3CMEH 1KQSH 1YI2H 3G6EH 1VQ4H 3CCVH 1VQ8H 4IOCJ 4UY8M 1W2BH 1K8AJ 1WKIA 1YITH 5GADN 3I55H 2ZJPJ 2QA4H 5GAHN 4WFAJ 3CMAH 3OW2H 4IOAJ 4IO9J 1Q81J 2OTLH 4WFBJ 1Y69K 3CC2H 1YJ9H 4WFNJ 5JVGJ 3CCRH 3CC4H 1VQOH 3J7ZM 5H1SO 4U67J 1K73J 3CCUH 3I56H 2OTJH 1Q82J 1YIJH 3CCJH 1M1KJ 1VQNH 5GAGN 1VQ5H 3G4SH 4WF9J 2ZJQJ 5AN9F 3CCSH 1VQPH 3PIPJ 5DM6J 1N8RJ 3CCMH 1YJNH 3DLLJ 2PA2A 5JVHJ 1QVGH 1VQMH 4WCEJ 1VQ9H 3CCLH 5GAEN 2ZJRJ 3CPWH 1KC8J 1VQKH 1JJ2H
chains in the Genus database with same CATH homology


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

 
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