5DM6E

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans
Total Genus 26
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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
26
sequence length
171
structure length
171
Chain Sequence
GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGK
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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 50S ribosomal protein L1
publication title Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
pubmed doi rcsb
total genus 26
structure length 171
sequence length 171
ec nomenclature
pdb deposition date 2015-09-08

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 5dm6E02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 5dm6E01
3CCQE 1YJNE 4WCEE 1Q81G 5GAEG 1VQKE 1VQME 3CC7E 1W2BE 2CQLA 3OW2E 3I55E 3PIPE 3CC4E 1S72E 5JVHE 4WFNE 3CC2E 1VQ9E 1VQ8E 3CCLE 2OTLE 2ZJPE 2QEXE 1YJ9E 5GAGG 3CMEE 2QA4E 5AN9B 3CCVE 1K73G 4U67E 1M90G 2ZJRE 3G6EE 4IO9E 1KQSE 5MLCH 4IOAE 5GADG 4WF9E 1YIJE 3CCJE 1VQ5E 5HL7E 3CD6E 1YI2E 1VQPE 1YJWE 3J7ZG 1K8AG 4WFBE 5DM7E 3G4SE 3CCUE 1Q7YG 2ZJQE 1YITE 1YHQE 1NJIG 1VQOE 1KD1G 1VQLE 1RL6A 1VQNE 1KC8G 1VQ6E 1M1KG 5JVGE 3DLLE 1QVGE 3CPWE 3PIOE 3CCEE 3CXCE 1JJ2E 1K9MG 1Q82G 1VQ7E 5DM6E 1VQ4E 5H1SI 3I56E 3CCME 3CCSE 4IOCE 1Q86G 3G71E 4UY8G 1QVFE 3CMAE 2OTJE 3CCRE 4WFAE 5GAHG 1N8RG 3CF5E
chains in the Genus database with same CATH superfamily
3CCQE 1YJNE 4WCEE 1Q81G 5GAEG 1VQKE 1VQME 3IGEA 3CKGA 3CC7E 1W2BE 3AUMO 2PI3O 2CQLA 2OY5O 3OW2E 3I55E 3PIPE 2OY8A 3CC4E 1S72E 5JVHE 4WFNE 2G8CO 3CC2E 1VQ9E 1VQ8E 2AF5A 3CCLE 2OTLE 2ZJPE 2QEXE 1YJ9E 5GAGG 3CMEE 2OL8O 2QA4E 5AN9B 3CCVE 1K73G 4U67E 1M90G 2ZJRE 3G6EE 4IO9E 1KQSE 5MLCH 4IOAE 5B3MO 5GADG 4WF9E 1RJLC 1YIJE 3CCJE 1VQ5E 5HL7E 3IG9A 3CD6E 1YI2E 2HKDA 1VQPE 1YJWE 3J7ZG 2I5VO 1K8AG 4WFBE 5DM7E 3G4SE 3EC5A 3CCUE 1Q7YG 2ZJQE 5B11O 2OYBO 2OY7A 1YITE 1YHQE 2I5ZO 1VQOE 1NJIG 1KD1G 1OSPO 1VQLE 1FJ1E 1RL6A 1VQNE 1KC8G 1VQ6E 1M1KG 5JVGE 3DLLE 3CKFA 1QVGE 2OY1O 2OL7A 3CPWE 2FKJA 3PIOE 3CCEE 2FKGA 3CXCE 1JJ2E 1K9MG 5B2AO 1Q82G 1VQ7E 5DM6E 1VQ4E 5H1SI 3I56E 3CCME 3CCSE 1P4PA 4IOCE 1Q86G 3G71E 4UY8G 1QVFE 2OL6O 3CMAE 2OTJE 5B10O 3CCRE 4WFAE 5GAHG 1N8RG 3CF5E
chains in the Genus database with same CATH topology
3CCQE 1YJNE 4WCEE 1Q81G 5GAEG 1VQKE 1VQME 3CC7E 1W2BE 2CQLA 3OW2E 3I55E 3PIPE 3CC4E 1S72E 5JVHE 4WFNE 3CC2E 1VQ9E 1VQ8E 3CCLE 2OTLE 2ZJPE 2QEXE 1YJ9E 5GAGG 3CMEE 2QA4E 5AN9B 3CCVE 1K73G 4U67E 1M90G 2ZJRE 3G6EE 4IO9E 1KQSE 5MLCH 4IOAE 5GADG 4WF9E 1YIJE 3CCJE 1VQ5E 5HL7E 3CD6E 1YI2E 1VQPE 1YJWE 3J7ZG 1K8AG 4WFBE 5DM7E 3G4SE 3CCUE 1Q7YG 2ZJQE 1YITE 1YHQE 1NJIG 1VQOE 1KD1G 1VQLE 1RL6A 1VQNE 1KC8G 1VQ6E 1M1KG 5JVGE 3DLLE 1QVGE 3CPWE 3PIOE 3CCEE 3CXCE 1JJ2E 1K9MG 1Q82G 1VQ7E 5DM6E 1VQ4E 5H1SI 3I56E 3CCME 3CCSE 4IOCE 1Q86G 3G71E 4UY8G 1QVFE 3CMAE 2OTJE 3CCRE 4WFAE 5GAHG 1N8RG 3CF5E
chains in the Genus database with same CATH homology


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