1VQLE

The structure of the transition state analogue "dcsn" 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
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 39
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 1vqlE02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vqlE01
3CCQE 1S72E 3G71E 2QA4E 3DLLE 1YITE 5DM7E 2QEXE 3CCLE 4WFNE 3I56E 1YHQE 1K9MG 3CC7E 5GAEG 1K8AG 5H1SI 5JVHE 1VQPE 5GAGG 3CD6E 1YJ9E 2OTLE 4IOAE 3OW2E 3CCEE 1Q86G 3G6EE 4UY8G 1VQ4E 1VQKE 1W2BE 2ZJPE 4WF9E 3CC4E 3PIPE 1VQ9E 5GAHG 1N8RG 1VQOE 5DM6E 5GADG 1YJWE 3CMAE 3PIOE 2ZJQE 3G4SE 3CC2E 1VQNE 1YI2E 1YJNE 4U67E 1QVFE 1VQLE 1YIJE 3CCSE 1NJIG 3J7ZG 1VQME 2OTJE 1Q7YG 3CF5E 3CCRE 3CXCE 3CCME 1KD1G 2CQLA 4IOCE 1M90G 3CMEE 1KC8G 5JVGE 3CCJE 1VQ7E 2ZJRE 1Q82G 1KQSE 1QVGE 4WFAE 1VQ5E 1VQ8E 3I55E 4WCEE 3CPWE 4IO9E 1Q81G 3CCVE 1M1KG 4WFBE 1RL6A 1JJ2E 5MLCH 1VQ6E 3CCUE 5HL7E 1K73G 5AN9B
chains in the Genus database with same CATH superfamily
3CCQE 2AF5A 1S72E 3G71E 2QA4E 2I5VO 3DLLE 1YITE 5DM7E 2QEXE 2FKJA 3CCLE 4WFNE 3I56E 1YHQE 1K9MG 3CC7E 5GAEG 1K8AG 5H1SI 5JVHE 5B11O 1VQPE 5GAGG 3CD6E 1YJ9E 2OY8A 2OTLE 3AUMO 4IOAE 3IG9A 3OW2E 3CCEE 1Q86G 3G6EE 4UY8G 5B2AO 1VQ4E 1VQKE 1W2BE 2ZJPE 4WF9E 3CC4E 1FJ1E 3PIPE 1VQ9E 5GAHG 2G8CO 1RJLC 1N8RG 1VQOE 5DM6E 5GADG 1YJWE 3CMAE 5B10O 3PIOE 2ZJQE 3G4SE 3CC2E 2FKGA 1VQNE 1YI2E 3IGEA 3EC5A 1YJNE 4U67E 1QVFE 1VQLE 1YIJE 2OL6O 3CCSE 1NJIG 3J7ZG 1VQME 2OTJE 2OL7A 5B3MO 1Q7YG 3CF5E 3CCRE 3CXCE 3CCME 1KD1G 2CQLA 4IOCE 1M90G 3CMEE 3CKGA 1KC8G 5JVGE 2OYBO 2PI3O 2OL8O 3CCJE 1VQ7E 2ZJRE 1Q82G 1KQSE 2OY7A 1QVGE 4WFAE 1VQ5E 1VQ8E 2OY1O 3I55E 4WCEE 1OSPO 3CPWE 4IO9E 2OY5O 1Q81G 3CCVE 1M1KG 1RL6A 1P4PA 4WFBE 2I5ZO 1JJ2E 5MLCH 1VQ6E 3CKFA 2HKDA 3CCUE 5HL7E 1K73G 5AN9B
chains in the Genus database with same CATH topology
3CCQE 1S72E 3G71E 2QA4E 3DLLE 1YITE 5DM7E 2QEXE 3CCLE 4WFNE 3I56E 1YHQE 1K9MG 3CC7E 5GAEG 1K8AG 5H1SI 5JVHE 1VQPE 5GAGG 3CD6E 1YJ9E 2OTLE 4IOAE 3OW2E 3CCEE 1Q86G 3G6EE 4UY8G 1VQ4E 1VQKE 1W2BE 2ZJPE 4WF9E 3CC4E 3PIPE 1VQ9E 5GAHG 1N8RG 1VQOE 5DM6E 5GADG 1YJWE 3CMAE 3PIOE 2ZJQE 3G4SE 3CC2E 1VQNE 1YI2E 1YJNE 4U67E 1QVFE 1VQLE 1YIJE 3CCSE 1NJIG 3J7ZG 1VQME 2OTJE 1Q7YG 3CF5E 3CCRE 3CXCE 3CCME 1KD1G 2CQLA 4IOCE 1M90G 3CMEE 1KC8G 5JVGE 3CCJE 1VQ7E 2ZJRE 1Q82G 1KQSE 1QVGE 4WFAE 1VQ5E 1VQ8E 3I55E 4WCEE 3CPWE 4IO9E 1Q81G 3CCVE 1M1KG 4WFBE 1RL6A 1JJ2E 5MLCH 1VQ6E 3CCUE 5HL7E 1K73G 5AN9B
chains in the Genus database with same CATH homology


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