5DM7E

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a
Total Genus 20
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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
20
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 20
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 5dm7E02
3.90.930.12 Alpha Beta Alpha-Beta Complex Outer Surface Protein A; domain 3 Ribosomal protein L6, alpha-beta domain 5dm7E01
4IOCE 3CC7E 1VQNE 1VQ6E 5GAHG 3CXCE 4IOAE 1VQLE 1KQSE 1K73G 5GADG 2QA4E 2ZJRE 3I56E 3CC4E 2ZJPE 1QVGE 3CF5E 5HL7E 1M90G 3CC2E 3CD6E 3PIPE 5DM7E 1VQME 1VQ5E 3CMEE 1VQ8E 1VQ7E 3CCRE 4WFBE 1VQ4E 3CCSE 5JVHE 1Q81G 1RL6A 1YJ9E 1Q82G 4IO9E 2ZJQE 1Q7YG 1Q86G 5DM6E 4U67E 3CCEE 5AN9B 1S72E 3CCVE 1VQPE 3I55E 1YITE 1N8RG 3CCLE 1YJNE 1K8AG 1QVFE 3PIOE 3CPWE 2CQLA 1VQOE 3CCUE 5GAGG 1YHQE 1YJWE 4WCEE 3CCME 2QEXE 5GAEG 1VQKE 5JVGE 5H1SI 1VQ9E 1M1KG 3J7ZG 4WF9E 5MLCH 3G6EE 3DLLE 1K9MG 3G4SE 1YI2E 4WFNE 1YIJE 3CCJE 3CMAE 4UY8G 1NJIG 2OTLE 3OW2E 2OTJE 3CCQE 1JJ2E 4WFAE 1KD1G 3G71E 1KC8G 1W2BE
chains in the Genus database with same CATH superfamily
4IOCE 3IG9A 3CC7E 1VQNE 1VQ6E 5GAHG 3CXCE 4IOAE 1P4PA 1VQLE 1KQSE 1K73G 5GADG 2QA4E 2OL7A 2HKDA 2ZJRE 3I56E 3CC4E 2ZJPE 1QVGE 3CF5E 5HL7E 1M90G 3CC2E 3CD6E 2FKJA 3PIPE 5DM7E 1VQME 1VQ5E 3CMEE 1VQ8E 1VQ7E 5B2AO 2OY1O 2PI3O 2G8CO 3CCRE 4WFBE 1VQ4E 3CCSE 5JVHE 1Q81G 1RL6A 1YJ9E 1Q82G 4IO9E 2ZJQE 1Q7YG 1Q86G 5DM6E 2OYBO 4U67E 3CCEE 5AN9B 2OY5O 1S72E 3CCVE 1VQPE 1RJLC 5B10O 3I55E 1YITE 1N8RG 3CCLE 1YJNE 1K8AG 1QVFE 3PIOE 3CPWE 2CQLA 3IGEA 3CKGA 1FJ1E 2OY8A 1VQOE 3CCUE 5GAGG 1YHQE 1YJWE 4WCEE 5B3MO 3CCME 2QEXE 2OL6O 5GAEG 1VQKE 5JVGE 5H1SI 1VQ9E 2I5ZO 1M1KG 3J7ZG 4WF9E 5MLCH 1OSPO 3G6EE 3DLLE 1K9MG 3G4SE 1YI2E 2I5VO 4WFNE 3AUMO 2OY7A 3CCJE 1YIJE 3CMAE 3CKFA 2OL8O 4UY8G 1NJIG 2OTLE 3OW2E 2OTJE 3CCQE 1JJ2E 4WFAE 1KD1G 3EC5A 3G71E 2AF5A 2FKGA 1KC8G 1W2BE 5B11O
chains in the Genus database with same CATH topology
4IOCE 3CC7E 1VQNE 1VQ6E 5GAHG 3CXCE 4IOAE 1VQLE 1KQSE 1K73G 5GADG 2QA4E 2ZJRE 3I56E 3CC4E 2ZJPE 1QVGE 3CF5E 5HL7E 1M90G 3CC2E 3CD6E 3PIPE 5DM7E 1VQME 1VQ5E 3CMEE 1VQ8E 1VQ7E 3CCRE 4WFBE 1VQ4E 3CCSE 5JVHE 1Q81G 1RL6A 1YJ9E 1Q82G 4IO9E 2ZJQE 1Q7YG 1Q86G 5DM6E 4U67E 3CCEE 5AN9B 1S72E 3CCVE 1VQPE 3I55E 1YITE 1N8RG 3CCLE 1YJNE 1K8AG 1QVFE 3PIOE 3CPWE 2CQLA 1VQOE 3CCUE 5GAGG 1YHQE 1YJWE 4WCEE 3CCME 2QEXE 5GAEG 1VQKE 5JVGE 5H1SI 1VQ9E 1M1KG 3J7ZG 4WF9E 5MLCH 3G6EE 3DLLE 1K9MG 3G4SE 1YI2E 4WFNE 1YIJE 3CCJE 3CMAE 4UY8G 1NJIG 2OTLE 3OW2E 2OTJE 3CCQE 1JJ2E 4WFAE 1KD1G 3G71E 1KC8G 1W2BE
chains in the Genus database with same CATH homology


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