1VQPE

The structure of the transition state analogue "rap" 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
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 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 1vqpE02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 1vqpE01
4U67E 1YI2E 1VQLE 4WFNE 3CC4E 1QVGE 3CCVE 1YHQE 3DLLE 3I56E 4UY8G 4IOAE 1YITE 5GAGG 1KQSE 1VQKE 1Q7YG 2ZJRE 1S72E 3PIPE 4WCEE 3CC7E 1VQ9E 3CCEE 1YJ9E 3CMAE 1VQ4E 3PIOE 1VQOE 1YJNE 5JVGE 1VQ5E 1VQ6E 2CQLA 5AN9B 1M1KG 3CCJE 4IOCE 5GADG 5GAEG 2OTLE 1N8RG 1VQ8E 3G6EE 1RL6A 1K9MG 1QVFE 3CC2E 3CCUE 3OW2E 1VQNE 3CXCE 3CCME 3CCSE 2ZJQE 4IO9E 3CCQE 5DM7E 3CF5E 1Q81G 5MLCH 4WFBE 1YIJE 1M90G 3G4SE 3CCLE 1W2BE 3G71E 5H1SI 1KC8G 3I55E 1K73G 5GAHG 1KD1G 3CPWE 5HL7E 2QEXE 5DM6E 2QA4E 1VQ7E 4WF9E 1Q82G 1VQPE 2ZJPE 1Q86G 1NJIG 1VQME 4WFAE 1YJWE 2OTJE 3J7ZG 3CCRE 3CMEE 5JVHE 3CD6E 1K8AG 1JJ2E
chains in the Genus database with same CATH superfamily
4U67E 2OY1O 1YI2E 1VQLE 4WFNE 3CC4E 1QVGE 3CCVE 1YHQE 2OYBO 3DLLE 3I56E 2I5ZO 3AUMO 4UY8G 4IOAE 1YITE 5GAGG 1KQSE 1VQKE 1Q7YG 1FJ1E 2ZJRE 2OL7A 2PI3O 3PIPE 1S72E 2OL8O 4WCEE 3CC7E 1VQ9E 3CCEE 1YJ9E 3CMAE 1VQ4E 5B2AO 3PIOE 1VQOE 1YJNE 5JVGE 1VQ5E 1VQ6E 2CQLA 5AN9B 1M1KG 3CCJE 4IOCE 5GADG 5GAEG 2OTLE 1N8RG 1VQ8E 3G6EE 1OSPO 1RL6A 1K9MG 5B11O 3CC2E 1QVFE 3CCUE 2OY8A 3OW2E 1VQNE 3CXCE 3CCME 3CCSE 2ZJQE 4IO9E 3IGEA 3CCQE 5DM7E 3CF5E 1Q81G 2FKGA 5MLCH 4WFBE 1YIJE 1M90G 3G4SE 3CCLE 1W2BE 3G71E 2HKDA 2AF5A 5H1SI 1KC8G 3I55E 5B3MO 1K73G 5GAHG 1KD1G 3CPWE 1P4PA 5HL7E 2QEXE 2I5VO 2G8CO 5DM6E 2QA4E 1VQ7E 4WF9E 1Q82G 1VQPE 2FKJA 2ZJPE 1Q86G 1NJIG 1RJLC 1VQME 4WFAE 1YJWE 3EC5A 2OTJE 3IG9A 3J7ZG 3CCRE 3CMEE 5JVHE 5B10O 3CKFA 3CD6E 3CKGA 2OY5O 2OY7A 1K8AG 1JJ2E 2OL6O
chains in the Genus database with same CATH topology
4U67E 1YI2E 1VQLE 4WFNE 3CC4E 1QVGE 3CCVE 1YHQE 3DLLE 3I56E 4UY8G 4IOAE 1YITE 5GAGG 1KQSE 1VQKE 1Q7YG 2ZJRE 1S72E 3PIPE 4WCEE 3CC7E 1VQ9E 3CCEE 1YJ9E 3CMAE 1VQ4E 3PIOE 1VQOE 1YJNE 5JVGE 1VQ5E 1VQ6E 2CQLA 5AN9B 1M1KG 3CCJE 4IOCE 5GADG 5GAEG 2OTLE 1N8RG 1VQ8E 3G6EE 1RL6A 1K9MG 1QVFE 3CC2E 3CCUE 3OW2E 1VQNE 3CXCE 3CCME 3CCSE 2ZJQE 4IO9E 3CCQE 5DM7E 3CF5E 1Q81G 5MLCH 4WFBE 1YIJE 1M90G 3G4SE 3CCLE 1W2BE 3G71E 5H1SI 1KC8G 3I55E 1K73G 5GAHG 1KD1G 3CPWE 5HL7E 2QEXE 5DM6E 2QA4E 1VQ7E 4WF9E 1Q82G 1VQPE 2ZJPE 1Q86G 1NJIG 1VQME 4WFAE 1YJWE 2OTJE 3J7ZG 3CCRE 3CMEE 5JVHE 3CD6E 1K8AG 1JJ2E
chains in the Genus database with same CATH homology


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