1VQ8E

The structure of ccda-phe-cap-bio and the antibiotic sparsomycin 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 1vq8E02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vq8E01
5GAEG 1VQME 1VQ8E 1VQLE 4IOAE 5JVGE 1QVGE 3CCLE 1NJIG 2ZJQE 1N8RG 1YHQE 5MLCH 3CCQE 1KD1G 3J7ZG 3CC7E 1VQPE 1VQ5E 5H1SI 3G71E 2ZJRE 1K8AG 1VQ4E 2QA4E 3CCRE 3CD6E 1VQ7E 3CCUE 1K73G 2OTLE 2ZJPE 5GAGG 3CCME 1VQOE 1M1KG 1YJWE 1VQ9E 2CQLA 5DM6E 1VQ6E 5GAHG 2QEXE 1Q7YG 3PIPE 1VQKE 3CC4E 3PIOE 1YI2E 1YIJE 3CCSE 5DM7E 3I55E 4IOCE 1YITE 1QVFE 3CPWE 3G6EE 4WFBE 3CCJE 2OTJE 5HL7E 1M90G 1S72E 4UY8G 3CCVE 5AN9B 4WFNE 3DLLE 1Q81G 3I56E 3CCEE 3CC2E 1KQSE 1YJ9E 5JVHE 5GADG 1VQNE 1Q82G 4WFAE 3CMAE 1Q86G 1RL6A 3OW2E 1KC8G 1W2BE 1K9MG 4IO9E 4WCEE 4U67E 3CXCE 3CMEE 4WF9E 1JJ2E 3G4SE 3CF5E 1YJNE
chains in the Genus database with same CATH superfamily
5GAEG 1VQME 1FJ1E 1VQ8E 1VQLE 2FKGA 4IOAE 5JVGE 1QVGE 2OL7A 3CCLE 1NJIG 3IG9A 2OY7A 2ZJQE 1N8RG 1YHQE 2OL6O 5MLCH 3CCQE 1KD1G 3CC7E 3CKFA 3J7ZG 1VQPE 1VQ5E 5H1SI 3G71E 1RJLC 2ZJRE 1K8AG 2I5ZO 1VQ4E 2QA4E 5B10O 3CCRE 3CD6E 2OY1O 1VQ7E 5B2AO 1OSPO 3CCUE 1K73G 2OTLE 2ZJPE 5GAGG 3CCME 1VQOE 3IGEA 2PI3O 1YJWE 1M1KG 1VQ9E 2CQLA 5DM6E 1VQ6E 2I5VO 5GAHG 2QEXE 1Q7YG 3PIPE 2FKJA 1VQKE 3CC4E 3PIOE 1YI2E 1YIJE 3CCSE 5DM7E 3I55E 4IOCE 1YITE 1QVFE 3CPWE 3G6EE 4WFBE 3CCJE 2OTJE 5HL7E 1M90G 3EC5A 1S72E 4UY8G 3AUMO 3CCVE 5AN9B 2AF5A 4WFNE 2OYBO 3DLLE 1Q81G 3CKGA 3I56E 3CCEE 3CC2E 1KQSE 1YJ9E 5JVHE 2OL8O 5GADG 1VQNE 1Q82G 4WFAE 3CMAE 1Q86G 2HKDA 1RL6A 1P4PA 3OW2E 1KC8G 1W2BE 5B3MO 1K9MG 4IO9E 4WCEE 5B11O 4U67E 3CXCE 2OY8A 3CMEE 4WF9E 1JJ2E 3G4SE 3CF5E 2G8CO 2OY5O 1YJNE
chains in the Genus database with same CATH topology
5GAEG 1VQME 1VQ8E 1VQLE 4IOAE 5JVGE 1QVGE 3CCLE 1NJIG 2ZJQE 1N8RG 1YHQE 5MLCH 3CCQE 1KD1G 3J7ZG 3CC7E 1VQPE 1VQ5E 5H1SI 3G71E 2ZJRE 1K8AG 1VQ4E 2QA4E 3CCRE 3CD6E 1VQ7E 3CCUE 1K73G 2OTLE 2ZJPE 5GAGG 3CCME 1VQOE 1M1KG 1YJWE 1VQ9E 2CQLA 5DM6E 1VQ6E 5GAHG 2QEXE 1Q7YG 3PIPE 1VQKE 3CC4E 3PIOE 1YI2E 1YIJE 3CCSE 5DM7E 3I55E 4IOCE 1YITE 1QVFE 3CPWE 3G6EE 4WFBE 3CCJE 2OTJE 5HL7E 1M90G 1S72E 4UY8G 3CCVE 5AN9B 4WFNE 3DLLE 1Q81G 3I56E 3CCEE 3CC2E 1KQSE 1YJ9E 5JVHE 5GADG 1VQNE 1Q82G 4WFAE 3CMAE 1Q86G 1RL6A 3OW2E 1KC8G 1W2BE 1K9MG 4IO9E 4WCEE 4U67E 3CXCE 3CMEE 4WF9E 1JJ2E 3G4SE 3CF5E 1YJNE
chains in the Genus database with same CATH homology


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