1VQPE

The structure of the transition state analogue "rap" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 38
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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
38
sequence length
172
structure length
172
Chain Sequence
b'PRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTMSTIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIHGDTDVEIDGEELTVSGPDIEAVGQTAADIEQLTRINDKDVRVFQDGVYITRKP'
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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 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
molecule tags Ribosome
total genus 38
structure length 172
sequence length 172
ec nomenclature
pdb deposition date 2004-12-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
E PF00347 Ribosomal_L6 Ribosomal protein L6
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vqpE02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vqpE01
3CCSE 5JVGE 3CCEE 4WFBE 1RL6A 3CF5E 3CCLE 1QVFE 3CPWE 5JVHE 1K73G 1M1KG 1S72E 5HL7E 1W2BE 3G6EE 1K8AG 1YIJE 1N8RG 2OTJE 3I55E 1YJWE 4WF9E 5MLCH 4U67E 3J7ZG 1VQ7E 3CMAE 3CD6E 4IO9E 4IOAE 1VQPE 1K9MG 1KQSE 5GAHG 3CCME 5GAGG 1KD1G 2QA4E 1VQLE 1YITE 1VQ4E 5AN9B 3I56E 1YI2E 1YJNE 1Q86G 1Q82G 4UY8G 3CC4E 2ZJRE 1NJIG 1Q7YG 4WCEE 3G4SE 1Q81G 5DM6E 4WFNE 3G71E 1JJ2E 3CC7E 1KC8G 5DM7E 4WFAE 1YHQE 3PIOE 2ZJPE 1M90G 3CCUE 3CCRE 3PIPE 2QEXE 3CCVE 1QVGE 5GADG 1VQ8E 3OW2E 1YJ9E 3DLLE 2OTLE 1VQKE 5H1SI 3CCJE 1VQOE 1VQME 5GAEG 2CQLA 3CMEE 1VQ6E 3CXCE 1VQ9E 1VQNE 3CC2E 4IOCE 2ZJQE 1VQ5E 3CCQE
chains in the Genus database with same CATH superfamily
2OL7A 3CCSE 5JVGE 2I5ZO 3CCEE 4WFBE 1P4PA 1RL6A 3CF5E 3CCLE 1QVFE 3CPWE 5JVHE 1K73G 1M1KG 1S72E 5HL7E 1W2BE 3G6EE 1K8AG 1YIJE 1N8RG 2OTJE 2AF5A 3I55E 3IG9A 1YJWE 4WF9E 5MLCH 4U67E 3J7ZG 1VQ7E 3CMAE 3CD6E 4IO9E 4IOAE 1VQPE 5B10O 1K9MG 5B3MO 1KQSE 5GAHG 2OYBO 2G8CO 3IGEA 3CCME 5GAGG 2OL8O 2OL6O 1RJLC 2OY1O 1KD1G 2QA4E 1VQLE 2OY5O 1YITE 1VQ4E 5AN9B 3I56E 1YI2E 1YJNE 1Q82G 1Q86G 4UY8G 3CC4E 5B2AO 3AUMO 2ZJRE 1NJIG 1Q7YG 4WCEE 3G4SE 2OY7A 1Q81G 5DM6E 4WFNE 3G71E 1JJ2E 3CC7E 2FKJA 1KC8G 5DM7E 4WFAE 1YHQE 3PIOE 1OSPO 2I5VO 2ZJPE 5B11O 2PI3O 1M90G 3CCUE 3CCRE 3PIPE 2QEXE 3CCVE 3CKGA 1QVGE 5GADG 1VQ8E 2FKGA 3OW2E 1YJ9E 3DLLE 2OTLE 1VQKE 5H1SI 2HKDA 3CCJE 2OY8A 1FJ1E 1VQOE 1VQME 3CKFA 5GAEG 2CQLA 3CMEE 1VQ6E 3CXCE 1VQ9E 1VQNE 3CC2E 4IOCE 3EC5A 2ZJQE 1VQ5E 3CCQE
chains in the Genus database with same CATH topology
3CCSE 5JVGE 3CCEE 4WFBE 1RL6A 3CF5E 3CCLE 1QVFE 3CPWE 5JVHE 1K73G 1M1KG 1S72E 5HL7E 1W2BE 3G6EE 1K8AG 1YIJE 1N8RG 2OTJE 3I55E 1YJWE 4WF9E 5MLCH 4U67E 3J7ZG 1VQ7E 3CMAE 3CD6E 4IO9E 4IOAE 1VQPE 1K9MG 1KQSE 5GAHG 3CCME 5GAGG 1KD1G 2QA4E 1VQLE 1YITE 1VQ4E 5AN9B 3I56E 1YI2E 1YJNE 1Q86G 1Q82G 4UY8G 3CC4E 2ZJRE 1NJIG 1Q7YG 4WCEE 3G4SE 1Q81G 5DM6E 4WFNE 3G71E 1JJ2E 3CC7E 1KC8G 5DM7E 4WFAE 1YHQE 3PIOE 2ZJPE 1M90G 3CCUE 3CCRE 3PIPE 2QEXE 3CCVE 1QVGE 5GADG 1VQ8E 3OW2E 1YJ9E 3DLLE 2OTLE 1VQKE 5H1SI 3CCJE 1VQOE 1VQME 5GAEG 2CQLA 3CMEE 1VQ6E 3CXCE 1VQ9E 1VQNE 3CC2E 4IOCE 2ZJQE 1VQ5E 3CCQE
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3CCS E;  5JVG E;  3CCE E;  4WFB E;  1RL6 A;  3CF5 E;  3CCL E;  1QVF E;  3CPW E;  5JVH E;  1K73 G;  1M1K G;  1S72 E;  5HL7 E;  1W2B E;  3G6E E;  1K8A G;  1YIJ E;  1N8R G;  2OTJ E;  3I55 E;  1YJW E;  4WF9 E;  5MLC H;  4U67 E;  3J7Z G;  1VQ7 E;  3CMA E;  3CD6 E;  4IO9 E;  4IOA E;  1VQP E;  1K9M G;  1KQS E;  5GAH G;  3CCM E;  5GAG G;  1KD1 G;  2QA4 E;  1VQL E;  1YIT E;  1VQ4 E;  5AN9 B;  3I56 E;  1YI2 E;  1YJN E;  1Q86 G;  1Q82 G;  4UY8 G;  3CC4 E;  2ZJR E;  1NJI G;  1Q7Y G;  4WCE E;  3G4S E;  1Q81 G;  5DM6 E;  4WFN E;  3G71 E;  1JJ2 E;  3CC7 E;  1KC8 G;  5DM7 E;  4WFA E;  1YHQ E;  3PIO E;  2ZJP E;  1M90 G;  3CCU E;  3CCR E;  3PIP E;  2QEX E;  3CCV E;  1QVG E;  5GAD G;  1VQ8 E;  3OW2 E;  1YJ9 E;  3DLL E;  2OTL E;  1VQK E;  5H1S I;  3CCJ E;  1VQO E;  1VQM E;  5GAE G;  2CQL A;  3CME E;  1VQ6 E;  3CXC E;  1VQ9 E;  1VQN E;  3CC2 E;  4IOC E;  2ZJQ E;  1VQ5 E;  3CCQ E; 
#chains in the Genus database with same CATH topology
 2OL7 A;  3CCS E;  5JVG E;  2I5Z O;  3CCE E;  4WFB E;  1P4P A;  1RL6 A;  3CF5 E;  3CCL E;  1QVF E;  3CPW E;  5JVH E;  1K73 G;  1M1K G;  1S72 E;  5HL7 E;  1W2B E;  3G6E E;  1K8A G;  1YIJ E;  1N8R G;  2OTJ E;  2AF5 A;  3I55 E;  3IG9 A;  1YJW E;  4WF9 E;  5MLC H;  4U67 E;  3J7Z G;  1VQ7 E;  3CMA E;  3CD6 E;  4IO9 E;  4IOA E;  1VQP E;  5B10 O;  1K9M G;  5B3M O;  1KQS E;  5GAH G;  2OYB O;  2G8C O;  3IGE A;  3CCM E;  5GAG G;  2OL8 O;  2OL6 O;  1RJL C;  2OY1 O;  1KD1 G;  2QA4 E;  1VQL E;  2OY5 O;  1YIT E;  1VQ4 E;  5AN9 B;  3I56 E;  1YI2 E;  1YJN E;  1Q82 G;  1Q86 G;  4UY8 G;  3CC4 E;  5B2A O;  3AUM O;  2ZJR E;  1NJI G;  1Q7Y G;  4WCE E;  3G4S E;  2OY7 A;  1Q81 G;  5DM6 E;  4WFN E;  3G71 E;  1JJ2 E;  3CC7 E;  2FKJ A;  1KC8 G;  5DM7 E;  4WFA E;  1YHQ E;  3PIO E;  1OSP O;  2I5V O;  2ZJP E;  5B11 O;  2PI3 O;  1M90 G;  3CCU E;  3CCR E;  3PIP E;  2QEX E;  3CCV E;  3CKG A;  1QVG E;  5GAD G;  1VQ8 E;  2FKG A;  3OW2 E;  1YJ9 E;  3DLL E;  2OTL E;  1VQK E;  5H1S I;  2HKD A;  3CCJ E;  2OY8 A;  1FJ1 E;  1VQO E;  1VQM E;  3CKF A;  5GAE G;  2CQL A;  3CME E;  1VQ6 E;  3CXC E;  1VQ9 E;  1VQN E;  3CC2 E;  4IOC E;  3EC5 A;  2ZJQ E;  1VQ5 E;  3CCQ E; 
#chains in the Genus database with same CATH homology
 3CCS E;  5JVG E;  3CCE E;  4WFB E;  1RL6 A;  3CF5 E;  3CCL E;  1QVF E;  3CPW E;  5JVH E;  1K73 G;  1M1K G;  1S72 E;  5HL7 E;  1W2B E;  3G6E E;  1K8A G;  1YIJ E;  1N8R G;  2OTJ E;  3I55 E;  1YJW E;  4WF9 E;  5MLC H;  4U67 E;  3J7Z G;  1VQ7 E;  3CMA E;  3CD6 E;  4IO9 E;  4IOA E;  1VQP E;  1K9M G;  1KQS E;  5GAH G;  3CCM E;  5GAG G;  1KD1 G;  2QA4 E;  1VQL E;  1YIT E;  1VQ4 E;  5AN9 B;  3I56 E;  1YI2 E;  1YJN E;  1Q86 G;  1Q82 G;  4UY8 G;  3CC4 E;  2ZJR E;  1NJI G;  1Q7Y G;  4WCE E;  3G4S E;  1Q81 G;  5DM6 E;  4WFN E;  3G71 E;  1JJ2 E;  3CC7 E;  1KC8 G;  5DM7 E;  4WFA E;  1YHQ E;  3PIO E;  2ZJP E;  1M90 G;  3CCU E;  3CCR E;  3PIP E;  2QEX E;  3CCV E;  1QVG E;  5GAD G;  1VQ8 E;  3OW2 E;  1YJ9 E;  3DLL E;  2OTL E;  1VQK E;  5H1S I;  3CCJ E;  1VQO E;  1VQM E;  5GAE G;  2CQL A;  3CME E;  1VQ6 E;  3CXC E;  1VQ9 E;  1VQN E;  3CC2 E;  4IOC E;  2ZJQ E;  1VQ5 E;  3CCQ E; 
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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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