1VQME

The structure of the transition state analogue "dan" 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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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
molecule keywords 23S ribosomal rna
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 1vqmE02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vqmE01
1K8AG 1VQME 1N8RG 1QVFE 2OTLE 3CC7E 1VQ5E 3G6EE 1YI2E 4WF9E 1Q86G 2ZJRE 2CQLA 1K9MG 1KQSE 1Q82G 1M90G 1W2BE 1NJIG 1VQPE 1QVGE 3CPWE 5JVHE 3I55E 3CCRE 3CCSE 5DM6E 2ZJPE 4IO9E 3I56E 4IOAE 4U67E 3OW2E 2ZJQE 1RL6A 1YJNE 3G71E 5AN9B 1KD1G 1YHQE 2OTJE 3CCLE 3CF5E 3CMAE 5MLCH 1VQOE 3CCEE 1VQNE 4UY8G 1VQLE 3PIOE 4WCEE 4IOCE 5DM7E 5GADG 3CD6E 1Q7YG 3CCUE 5GAHG 5GAEG 3PIPE 1KC8G 1VQ7E 2QA4E 1VQ4E 3DLLE 5JVGE 3CCJE 1M1KG 2QEXE 5GAGG 3CXCE 1YJWE 3G4SE 3CCVE 1YITE 4WFNE 3CCME 3CC2E 1Q81G 3CC4E 5HL7E 3J7ZG 1VQ8E 5H1SI 4WFAE 1JJ2E 1YIJE 1YJ9E 1S72E 4WFBE 1K73G 1VQ9E 1VQKE 1VQ6E 3CMEE 3CCQE
chains in the Genus database with same CATH superfamily
1K8AG 1VQME 1RJLC 1N8RG 1QVFE 2OL8O 2OY7A 3CC7E 2OTLE 5B2AO 3IG9A 1VQ5E 3G6EE 1YI2E 4WF9E 1Q86G 2ZJRE 2CQLA 1K9MG 1P4PA 1KQSE 1Q82G 1M90G 1W2BE 2FKJA 1NJIG 1VQPE 1QVGE 3CPWE 5JVHE 3I55E 3CCRE 3CCSE 5DM6E 2ZJPE 5B11O 4IO9E 3I56E 4IOAE 4U67E 2OYBO 3OW2E 2ZJQE 1RL6A 2AF5A 2FKGA 3G71E 1YJNE 5AN9B 1KD1G 1YHQE 2OTJE 3CCLE 3CF5E 3CMAE 5MLCH 1VQOE 3CCEE 1VQNE 4UY8G 1VQLE 3PIOE 4WCEE 3AUMO 2I5VO 4IOCE 2OL6O 5DM7E 5GADG 3CD6E 1Q7YG 3CCUE 5GAHG 2PI3O 3CKGA 5GAEG 3PIPE 1KC8G 1VQ7E 2QA4E 1VQ4E 3DLLE 5JVGE 2HKDA 3CCJE 1M1KG 2QEXE 5GAGG 3CXCE 3EC5A 5B10O 1YJWE 3G4SE 3CCVE 1YITE 4WFNE 5B3MO 3CCME 2OY1O 3CC2E 1Q81G 2G8CO 1FJ1E 2I5ZO 3CC4E 5HL7E 3J7ZG 1VQ8E 5H1SI 4WFAE 1JJ2E 2OL7A 1YIJE 3IGEA 1YJ9E 1S72E 4WFBE 1K73G 1VQ9E 1VQKE 1VQ6E 3CKFA 1OSPO 3CMEE 3CCQE 2OY8A 2OY5O
chains in the Genus database with same CATH topology
1K8AG 1VQME 1N8RG 1QVFE 2OTLE 3CC7E 1VQ5E 3G6EE 1YI2E 4WF9E 1Q86G 2ZJRE 2CQLA 1K9MG 1KQSE 1Q82G 1M90G 1W2BE 1NJIG 1VQPE 1QVGE 3CPWE 5JVHE 3I55E 3CCRE 3CCSE 5DM6E 2ZJPE 4IO9E 3I56E 4IOAE 4U67E 3OW2E 2ZJQE 1RL6A 1YJNE 3G71E 5AN9B 1KD1G 1YHQE 2OTJE 3CCLE 3CF5E 3CMAE 5MLCH 1VQOE 3CCEE 1VQNE 4UY8G 1VQLE 3PIOE 4WCEE 4IOCE 5DM7E 5GADG 3CD6E 1Q7YG 3CCUE 5GAHG 5GAEG 3PIPE 1KC8G 1VQ7E 2QA4E 1VQ4E 3DLLE 5JVGE 3CCJE 1M1KG 2QEXE 5GAGG 3CXCE 1YJWE 3G4SE 3CCVE 1YITE 4WFNE 3CCME 3CC2E 1Q81G 3CC4E 5HL7E 3J7ZG 1VQ8E 5H1SI 4WFAE 1JJ2E 1YIJE 1YJ9E 1S72E 4WFBE 1K73G 1VQ9E 1VQKE 1VQ6E 3CMEE 3CCQE
chains in the Genus database with same CATH homology


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