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


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