3G6ED

Co-crystal structure of homoharringtonine bound to the large ribosomal subunit
Total Genus 15
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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
15
sequence length
165
structure length
140
Chain Sequence
FHEMREPRIEKVVVHMGIGHANAEDILGEITGQMPVRTKAKRTVGEFDIREGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGLDVTVNLVRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEV
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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 U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
pubmed doi rcsb
total genus 15
structure length 140
sequence length 165
ec nomenclature
pdb deposition date 2009-02-06

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF00281 Ribosomal_L5 Ribosomal protein L5
D PF00673 Ribosomal_L5_C ribosomal L5P family C-terminus
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.1440.10 Alpha Beta 2-Layer Sandwich 50s Ribosomal Protein L5; Chain: A, 50s Ribosomal Protein L5; Chain: A, 3g6eD00
4U67D 1Q82F 1VQLD 1YJND 1K8AF 5GAGF 4WFND 1VQPD 3CCRD 3PIOD 1YHQD 4WFBD 3CCVD 3I56D 1VQ7D 1VQ6D 2OTLD 2NRQA 2PZZA 1KD1F 2QEXD 5HL7D 3PIPD 1VQND 1YJ9D 3G4SD 4IOCD 1Q81F 1Q86F 1K73F 1QVFD 1JJ2D 5H1SH 5DM6D 1VQ8D 1K9MF 4WFAD 1W2BD 5GADF 3CCMD 3G6ED 2NWUA 3CCQD 3C9GA 2WNYA 3OW2D 1NJIF 1KC8F 2QA4D 2OTJD 3CCED 5MLCG 1IQ4A 5JVGD 1VQOD 1VQ9D 1YIJD 3CXCD 1VQMD 3I55D 1M90F 3J7ZF 3CC2D 2OGKA 3CCSD 1VQKD 2ZJPD 3CMAD 3DLLD 3CC7D 1KQSD 3G71D 1YI2D 1Q7YF 1N8RF 5JVHD 3CCLD 1MJIA 3CCUD 3D7AA 2ZJRD 3CCJD 1YITD 4UY8F 5GAEF 3CF5D 4WF9D 4IO9D 1QVGD 3CPWD 4WCED 3CD6D 1YJWD 3CMED 1M1KF 1VQ5D 5GAHF 1S72D 2ZJQD 4IOAD 3CC4D 5DM7D 1VQ4D
chains in the Genus database with same CATH superfamily
4U67D 1Q82F 1VQLD 1YJND 1K8AF 5GAGF 4WFND 1VQPD 3CCRD 3PIOD 1YHQD 4WFBD 3CCVD 3I56D 1VQ7D 1VQ6D 2OTLD 2NRQA 2PZZA 1KD1F 2QEXD 5HL7D 3PIPD 1VQND 1YJ9D 3G4SD 4IOCD 1Q81F 1Q86F 1K73F 1QVFD 1JJ2D 5H1SH 5DM6D 1VQ8D 1K9MF 4WFAD 1W2BD 5GADF 3CCMD 3G6ED 2NWUA 3CCQD 3C9GA 2WNYA 3OW2D 1NJIF 1KC8F 2QA4D 2OTJD 3CCED 5MLCG 1IQ4A 5JVGD 1VQOD 1VQ9D 1YIJD 3CXCD 1VQMD 3I55D 1M90F 3J7ZF 3CC2D 2OGKA 3CCSD 1VQKD 2ZJPD 3CMAD 3DLLD 3CC7D 1KQSD 3G71D 1YI2D 1Q7YF 1N8RF 5JVHD 3CCLD 1MJIA 3CCUD 3D7AA 2ZJRD 3CCJD 1YITD 4UY8F 5GAEF 3CF5D 4WF9D 4IO9D 1QVGD 3CPWD 4WCED 3CD6D 1YJWD 3CMED 1M1KF 1VQ5D 5GAHF 1S72D 2ZJQD 4IOAD 3CC4D 5DM7D 1VQ4D
chains in the Genus database with same CATH topology
4U67D 1Q82F 1VQLD 1YJND 1K8AF 5GAGF 4WFND 1VQPD 3CCRD 3PIOD 1YHQD 4WFBD 3CCVD 3I56D 1VQ7D 1VQ6D 2OTLD 2NRQA 2PZZA 1KD1F 2QEXD 5HL7D 3PIPD 1VQND 1YJ9D 3G4SD 4IOCD 1Q81F 1Q86F 1K73F 1QVFD 1JJ2D 5H1SH 5DM6D 1VQ8D 1K9MF 4WFAD 1W2BD 5GADF 3CCMD 3G6ED 2NWUA 3CCQD 3C9GA 2WNYA 3OW2D 1NJIF 1KC8F 2QA4D 2OTJD 3CCED 5MLCG 1IQ4A 5JVGD 1VQOD 1VQ9D 1YIJD 3CXCD 1VQMD 3I55D 1M90F 3J7ZF 3CC2D 2OGKA 3CCSD 1VQKD 2ZJPD 3CMAD 3DLLD 3CC7D 1KQSD 3G71D 1YI2D 1Q7YF 1N8RF 5JVHD 3CCLD 1MJIA 3CCUD 3D7AA 2ZJRD 3CCJD 1YITD 4UY8F 5GAEF 3CF5D 4WF9D 4IO9D 1QVGD 3CPWD 4WCED 3CD6D 1YJWD 3CMED 1M1KF 1VQ5D 5GAHF 1S72D 2ZJQD 4IOAD 3CC4D 5DM7D 1VQ4D
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4U67 D;  1Q82 F;  1VQL D;  1YJN D;  1K8A F;  5GAG F;  4WFN D;  1VQP D;  3CCR D;  3PIO D;  1YHQ D;  4WFB D;  3CCV D;  3I56 D;  1VQ7 D;  1VQ6 D;  2OTL D;  2NRQ A;  2PZZ A;  1KD1 F;  2QEX D;  5HL7 D;  3PIP D;  1VQN D;  1YJ9 D;  3G4S D;  4IOC D;  1Q81 F;  1Q86 F;  1K73 F;  1QVF D;  1JJ2 D;  5H1S H;  5DM6 D;  1VQ8 D;  1K9M F;  4WFA D;  1W2B D;  5GAD F;  3CCM D;  3G6E D;  2NWU A;  3CCQ D;  3C9G A;  2WNY A;  3OW2 D;  1NJI F;  1KC8 F;  2QA4 D;  2OTJ D;  3CCE D;  5MLC G;  1IQ4 A;  5JVG D;  1VQO D;  1VQ9 D;  1YIJ D;  3CXC D;  1VQM D;  3I55 D;  1M90 F;  3J7Z F;  3CC2 D;  2OGK A;  3CCS D;  1VQK D;  2ZJP D;  3CMA D;  3DLL D;  3CC7 D;  1KQS D;  3G71 D;  1YI2 D;  1Q7Y F;  1N8R F;  5JVH D;  3CCL D;  1MJI A;  3CCU D;  3D7A A;  2ZJR D;  3CCJ D;  1YIT D;  4UY8 F;  5GAE F;  3CF5 D;  4WF9 D;  4IO9 D;  1QVG D;  3CPW D;  4WCE D;  3CD6 D;  1YJW D;  3CME D;  1M1K F;  1VQ5 D;  5GAH F;  1S72 D;  2ZJQ D;  4IOA D;  3CC4 D;  5DM7 D;  1VQ4 D; 
#chains in the Genus database with same CATH topology
 4U67 D;  1Q82 F;  1VQL D;  1YJN D;  1K8A F;  5GAG F;  4WFN D;  1VQP D;  3CCR D;  3PIO D;  1YHQ D;  4WFB D;  3CCV D;  3I56 D;  1VQ7 D;  1VQ6 D;  2OTL D;  2NRQ A;  2PZZ A;  1KD1 F;  2QEX D;  5HL7 D;  3PIP D;  1VQN D;  1YJ9 D;  3G4S D;  4IOC D;  1Q81 F;  1Q86 F;  1K73 F;  1QVF D;  1JJ2 D;  5H1S H;  5DM6 D;  1VQ8 D;  1K9M F;  4WFA D;  1W2B D;  5GAD F;  3CCM D;  3G6E D;  2NWU A;  3CCQ D;  3C9G A;  2WNY A;  3OW2 D;  1NJI F;  1KC8 F;  2QA4 D;  2OTJ D;  3CCE D;  5MLC G;  1IQ4 A;  5JVG D;  1VQO D;  1VQ9 D;  1YIJ D;  3CXC D;  1VQM D;  3I55 D;  1M90 F;  3J7Z F;  3CC2 D;  2OGK A;  3CCS D;  1VQK D;  2ZJP D;  3CMA D;  3DLL D;  3CC7 D;  1KQS D;  3G71 D;  1YI2 D;  1Q7Y F;  1N8R F;  5JVH D;  3CCL D;  1MJI A;  3CCU D;  3D7A A;  2ZJR D;  3CCJ D;  1YIT D;  4UY8 F;  5GAE F;  3CF5 D;  4WF9 D;  4IO9 D;  1QVG D;  3CPW D;  4WCE D;  3CD6 D;  1YJW D;  3CME D;  1M1K F;  1VQ5 D;  5GAH F;  1S72 D;  2ZJQ D;  4IOA D;  3CC4 D;  5DM7 D;  1VQ4 D; 
#chains in the Genus database with same CATH homology
 4U67 D;  1Q82 F;  1VQL D;  1YJN D;  1K8A F;  5GAG F;  4WFN D;  1VQP D;  3CCR D;  3PIO D;  1YHQ D;  4WFB D;  3CCV D;  3I56 D;  1VQ7 D;  1VQ6 D;  2OTL D;  2NRQ A;  2PZZ A;  1KD1 F;  2QEX D;  5HL7 D;  3PIP D;  1VQN D;  1YJ9 D;  3G4S D;  4IOC D;  1Q81 F;  1Q86 F;  1K73 F;  1QVF D;  1JJ2 D;  5H1S H;  5DM6 D;  1VQ8 D;  1K9M F;  4WFA D;  1W2B D;  5GAD F;  3CCM D;  3G6E D;  2NWU A;  3CCQ D;  3C9G A;  2WNY A;  3OW2 D;  1NJI F;  1KC8 F;  2QA4 D;  2OTJ D;  3CCE D;  5MLC G;  1IQ4 A;  5JVG D;  1VQO D;  1VQ9 D;  1YIJ D;  3CXC D;  1VQM D;  3I55 D;  1M90 F;  3J7Z F;  3CC2 D;  2OGK A;  3CCS D;  1VQK D;  2ZJP D;  3CMA D;  3DLL D;  3CC7 D;  1KQS D;  3G71 D;  1YI2 D;  1Q7Y F;  1N8R F;  5JVH D;  3CCL D;  1MJI A;  3CCU D;  3D7A A;  2ZJR D;  3CCJ D;  1YIT D;  4UY8 F;  5GAE F;  3CF5 D;  4WF9 D;  4IO9 D;  1QVG D;  3CPW D;  4WCE D;  3CD6 D;  1YJW D;  3CME D;  1M1K F;  1VQ5 D;  5GAH F;  1S72 D;  2ZJQ D;  4IOA D;  3CC4 D;  5DM7 D;  1VQ4 D; 
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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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#similar chains in the pdb database (?% sequence similarity)
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