2OTLD

Girodazole bound to the large subunit of haloarcula marismortui
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
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 The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole.
pubmed doi rcsb
total genus 20
structure length 140
sequence length 165
ec nomenclature
pdb deposition date 2007-02-08

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, 2otlD00
2QEXD 1M1KF 3CCUD 3CCMD 5MLCG 2QA4D 1S72D 4IO9D 1VQPD 2OTJD 1K8AF 1VQMD 2ZJRD 5GAEF 1YJWD 2WNYA 3G4SD 1VQKD 5GAHF 3CCVD 4IOAD 5GADF 2ZJPD 5HL7D 3CMED 1W2BD 3OW2D 1VQ8D 3CCJD 1Q81F 1VQOD 3PIOD 5DM6D 2ZJQD 3CD6D 3G6ED 3CXCD 1VQ9D 3CC7D 1YJND 4WF9D 1NJIF 3CC2D 3C9GA 5JVGD 1VQ4D 1IQ4A 1QVFD 4WFAD 3D7AA 4IOCD 3CMAD 1KC8F 4WFBD 3CC4D 1Q82F 2PZZA 1YI2D 3CCQD 1YJ9D 4WFND 1VQND 5GAGF 3CCSD 3CCLD 2OGKA 1KD1F 1JJ2D 5DM7D 1N8RF 5JVHD 3J7ZF 1K73F 3CF5D 2NWUA 2OTLD 1Q7YF 3CPWD 1VQLD 3DLLD 1VQ6D 3PIPD 1YHQD 3I56D 1KQSD 1VQ7D 1VQ5D 3I55D 4U67D 4UY8F 1YIJD 4WCED 1MJIA 3CCED 1QVGD 1Q86F 2NRQA 1YITD 3G71D 3CCRD 5H1SH 1M90F 1K9MF
chains in the Genus database with same CATH superfamily
2QEXD 1M1KF 3CCUD 3CCMD 5MLCG 2QA4D 1S72D 4IO9D 1VQPD 2OTJD 1K8AF 1VQMD 2ZJRD 5GAEF 1YJWD 2WNYA 3G4SD 1VQKD 5GAHF 3CCVD 4IOAD 5GADF 2ZJPD 5HL7D 3CMED 1W2BD 3OW2D 1VQ8D 3CCJD 1Q81F 1VQOD 3PIOD 5DM6D 2ZJQD 3CD6D 3G6ED 3CXCD 1VQ9D 3CC7D 1YJND 4WF9D 1NJIF 3CC2D 3C9GA 5JVGD 1VQ4D 1IQ4A 1QVFD 4WFAD 3D7AA 4IOCD 3CMAD 1KC8F 4WFBD 3CC4D 1Q82F 2PZZA 1YI2D 3CCQD 1YJ9D 4WFND 1VQND 5GAGF 3CCSD 3CCLD 2OGKA 1KD1F 1JJ2D 5DM7D 1N8RF 5JVHD 3J7ZF 1K73F 3CF5D 2NWUA 2OTLD 1Q7YF 3CPWD 1VQLD 3DLLD 1VQ6D 3PIPD 1YHQD 3I56D 1KQSD 1VQ7D 1VQ5D 3I55D 4U67D 4UY8F 1YIJD 4WCED 1MJIA 3CCED 1QVGD 1Q86F 2NRQA 1YITD 3G71D 3CCRD 5H1SH 1M90F 1K9MF
chains in the Genus database with same CATH topology
2QEXD 1M1KF 3CCUD 3CCMD 5MLCG 2QA4D 1S72D 4IO9D 1VQPD 2OTJD 1K8AF 1VQMD 2ZJRD 5GAEF 1YJWD 2WNYA 3G4SD 1VQKD 5GAHF 3CCVD 4IOAD 5GADF 2ZJPD 5HL7D 3CMED 1W2BD 3OW2D 1VQ8D 3CCJD 1Q81F 1VQOD 3PIOD 5DM6D 2ZJQD 3CD6D 3G6ED 3CXCD 1VQ9D 3CC7D 1YJND 4WF9D 1NJIF 3CC2D 3C9GA 5JVGD 1VQ4D 1IQ4A 1QVFD 4WFAD 3D7AA 4IOCD 3CMAD 1KC8F 4WFBD 3CC4D 1Q82F 2PZZA 1YI2D 3CCQD 1YJ9D 4WFND 1VQND 5GAGF 3CCSD 3CCLD 2OGKA 1KD1F 1JJ2D 5DM7D 1N8RF 5JVHD 3J7ZF 1K73F 3CF5D 2NWUA 2OTLD 1Q7YF 3CPWD 1VQLD 3DLLD 1VQ6D 3PIPD 1YHQD 3I56D 1KQSD 1VQ7D 1VQ5D 3I55D 4U67D 4UY8F 1YIJD 4WCED 1MJIA 3CCED 1QVGD 1Q86F 2NRQA 1YITD 3G71D 3CCRD 5H1SH 1M90F 1K9MF
chains in the Genus database with same CATH homology


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