1VQ4E

The structure of the transition state analogue "daa" 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 1vq4E02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vq4E01
4WFBE 4IO9E 3CCLE 1S72E 1VQ5E 1QVFE 1Q82G 3CMEE 5GAEG 1RL6A 5H1SI 1YJNE 1YJ9E 3CCQE 5AN9B 1VQ9E 3CCME 1VQ8E 5MLCH 1M1KG 1K9MG 3I55E 1YHQE 1K8AG 5GAGG 4WCEE 1QVGE 3G4SE 2CQLA 5GAHG 5JVGE 1YI2E 1W2BE 2QA4E 1NJIG 1Q7YG 3CCRE 4WF9E 3PIOE 5DM7E 1YITE 1VQLE 1Q81G 3CCJE 4WFAE 1JJ2E 3CD6E 3G6EE 1VQPE 3CXCE 3CC4E 1KC8G 3CCEE 4WFNE 1KQSE 2ZJRE 3G71E 4IOCE 3CPWE 3PIPE 3CF5E 1K73G 1YJWE 1KD1G 2OTJE 2OTLE 1VQ6E 1VQ4E 1YIJE 3DLLE 5JVHE 2ZJPE 4IOAE 4U67E 3CC7E 5GADG 5HL7E 2QEXE 3OW2E 3I56E 1VQOE 3CCUE 1VQNE 1VQ7E 5DM6E 3CMAE 1VQKE 2ZJQE 1VQME 4UY8G 1N8RG 3J7ZG 1Q86G 1M90G 3CC2E 3CCVE 3CCSE
chains in the Genus database with same CATH superfamily
4WFBE 4IO9E 3CCLE 1S72E 1VQ5E 1QVFE 1Q82G 3CMEE 5GAEG 1RL6A 5H1SI 1YJNE 1YJ9E 3CCQE 5AN9B 1VQ9E 3CCME 1VQ8E 5MLCH 1P4PA 3IG9A 1M1KG 2FKJA 1K9MG 3I55E 1YHQE 1K8AG 2HKDA 5GAGG 4WCEE 1QVGE 3G4SE 1OSPO 2CQLA 5GAHG 5JVGE 1YI2E 1W2BE 2PI3O 2QA4E 1NJIG 5B11O 1Q7YG 3CCRE 2OY8A 3PIOE 5DM7E 4WF9E 1YITE 1VQLE 3CKFA 1Q81G 5B10O 5B3MO 2I5ZO 3CCJE 4WFAE 1JJ2E 3CD6E 3G6EE 2FKGA 1FJ1E 3CKGA 1VQPE 3AUMO 1RJLC 3CXCE 3CC4E 2OYBO 1KC8G 3CCEE 4WFNE 2OY7A 1KQSE 2ZJRE 3G71E 4IOCE 3CPWE 3PIPE 3CF5E 1K73G 1YJWE 1KD1G 2OTJE 2OTLE 1VQ6E 2OY5O 1VQ4E 1YIJE 2OL6O 3DLLE 5JVHE 2ZJPE 4IOAE 4U67E 3CC7E 5GADG 2AF5A 5HL7E 2QEXE 3OW2E 3IGEA 3I56E 5B2AO 1VQOE 3CCUE 1VQNE 2OL8O 1VQ7E 5DM6E 3CMAE 1VQKE 2OY1O 2ZJQE 1VQME 4UY8G 1N8RG 2OL7A 3J7ZG 2I5VO 1Q86G 1M90G 3CC2E 2G8CO 3CCVE 3CCSE 3EC5A
chains in the Genus database with same CATH topology
4WFBE 4IO9E 3CCLE 1S72E 1VQ5E 1QVFE 1Q82G 3CMEE 5GAEG 1RL6A 5H1SI 1YJNE 1YJ9E 3CCQE 5AN9B 1VQ9E 3CCME 1VQ8E 5MLCH 1M1KG 1K9MG 3I55E 1YHQE 1K8AG 5GAGG 4WCEE 1QVGE 3G4SE 2CQLA 5GAHG 5JVGE 1YI2E 1W2BE 2QA4E 1NJIG 1Q7YG 3CCRE 4WF9E 3PIOE 5DM7E 1YITE 1VQLE 1Q81G 3CCJE 4WFAE 1JJ2E 3CD6E 3G6EE 1VQPE 3CXCE 3CC4E 1KC8G 3CCEE 4WFNE 1KQSE 2ZJRE 3G71E 4IOCE 3CPWE 3PIPE 3CF5E 1K73G 1YJWE 1KD1G 2OTJE 2OTLE 1VQ6E 1VQ4E 1YIJE 3DLLE 5JVHE 2ZJPE 4IOAE 4U67E 3CC7E 5GADG 5HL7E 2QEXE 3OW2E 3I56E 1VQOE 3CCUE 1VQNE 1VQ7E 5DM6E 3CMAE 1VQKE 2ZJQE 1VQME 4UY8G 1N8RG 3J7ZG 1Q86G 1M90G 3CC2E 3CCVE 3CCSE
chains in the Genus database with same CATH homology


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