1VQ5E

The structure of the transition state analogue "raa" 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 1vq5E02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vq5E01
1YI2E 3G6EE 1VQ4E 3I56E 3PIPE 3CCUE 1KC8G 5GAEG 1YITE 4WF9E 1YJWE 1K9MG 3CC4E 5GAHG 5DM6E 4WFAE 3CCJE 3DLLE 4IO9E 1Q7YG 5DM7E 1Q82G 2QEXE 4WFNE 3CCME 3CC7E 4U67E 4UY8G 3CD6E 3CPWE 2OTLE 3PIOE 3J7ZG 1YHQE 1VQKE 3CCLE 3CCSE 1S72E 1KD1G 1K73G 3CF5E 4IOCE 2ZJQE 2ZJPE 1VQME 1QVGE 5MLCH 5AN9B 3CXCE 2QA4E 5HL7E 1VQ6E 2OTJE 5GAGG 1Q86G 4WFBE 1VQ8E 1NJIG 3CCEE 3G4SE 5JVGE 3I55E 1M90G 1YJ9E 1K8AG 3CCQE 1M1KG 3CCRE 3CCVE 1JJ2E 3CMAE 5GADG 1VQOE 5JVHE 1W2BE 1RL6A 1VQLE 2CQLA 1VQ9E 4WCEE 3CMEE 3OW2E 1Q81G 2ZJRE 1YIJE 1N8RG 1QVFE 1YJNE 1VQ7E 1VQ5E 1KQSE 1VQNE 1VQPE 4IOAE 3G71E 5H1SI 3CC2E
chains in the Genus database with same CATH superfamily
1YI2E 3G6EE 1VQ4E 3I56E 5B11O 3PIPE 3CCUE 1KC8G 5GAEG 1YITE 4WF9E 2G8CO 1YJWE 3CC4E 2I5ZO 2OYBO 5DM6E 5GAHG 1K9MG 5B2AO 4WFAE 3CCJE 3AUMO 3DLLE 4IO9E 2AF5A 1Q7YG 5DM7E 2OL7A 1Q82G 2QEXE 4WFNE 3CCME 3CC7E 2OL6O 4U67E 4UY8G 3CD6E 3CPWE 3IGEA 2OTLE 3CKFA 3PIOE 3J7ZG 2OY7A 1YHQE 1VQKE 2FKJA 3CCLE 3CCSE 1S72E 1KD1G 1K73G 3CF5E 4IOCE 1P4PA 2ZJQE 2ZJPE 1VQME 1QVGE 5MLCH 5AN9B 5B3MO 3CXCE 2OY8A 2QA4E 5HL7E 1VQ6E 2HKDA 2OTJE 5GAGG 1Q86G 4WFBE 3IG9A 1VQ8E 1NJIG 3CCEE 3G4SE 1OSPO 5JVGE 3I55E 1FJ1E 2FKGA 1M90G 1YJ9E 1RJLC 1K8AG 5B10O 3CCQE 1M1KG 3CCRE 3CCVE 1JJ2E 2OY5O 3CMAE 5GADG 1VQOE 5JVHE 1W2BE 1RL6A 1VQLE 3CKGA 2CQLA 1VQ9E 4WCEE 3CMEE 3OW2E 2OL8O 1Q81G 2ZJRE 1YIJE 2I5VO 1N8RG 1QVFE 1YJNE 1VQ7E 1VQ5E 1KQSE 2OY1O 1VQNE 1VQPE 3EC5A 4IOAE 3G71E 2PI3O 5H1SI 3CC2E
chains in the Genus database with same CATH topology
1YI2E 3G6EE 1VQ4E 3I56E 3PIPE 3CCUE 1KC8G 5GAEG 1YITE 4WF9E 1YJWE 1K9MG 3CC4E 5GAHG 5DM6E 4WFAE 3CCJE 3DLLE 4IO9E 1Q7YG 5DM7E 1Q82G 2QEXE 4WFNE 3CCME 3CC7E 4U67E 4UY8G 3CD6E 3CPWE 2OTLE 3PIOE 3J7ZG 1YHQE 1VQKE 3CCLE 3CCSE 1S72E 1KD1G 1K73G 3CF5E 4IOCE 2ZJQE 2ZJPE 1VQME 1QVGE 5MLCH 5AN9B 3CXCE 2QA4E 5HL7E 1VQ6E 2OTJE 5GAGG 1Q86G 4WFBE 1VQ8E 1NJIG 3CCEE 3G4SE 5JVGE 3I55E 1M90G 1YJ9E 1K8AG 3CCQE 1M1KG 3CCRE 3CCVE 1JJ2E 3CMAE 5GADG 1VQOE 5JVHE 1W2BE 1RL6A 1VQLE 2CQLA 1VQ9E 4WCEE 3CMEE 3OW2E 1Q81G 2ZJRE 1YIJE 1N8RG 1QVFE 1YJNE 1VQ7E 1VQ5E 1KQSE 1VQNE 1VQPE 4IOAE 3G71E 5H1SI 3CC2E
chains in the Genus database with same CATH homology


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