5DM7D

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a
Total Genus 32
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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
32
sequence length
177
structure length
177
Chain Sequence
QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDKAAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEKLINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGMDITIVTTAKTDEEARALLQSMGLPFRK
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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 32
structure length 177
sequence length 177
ec nomenclature
pdb deposition date 2015-09-08

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, 5dm7D00
3CCJD 4U67D 3CC7D 2OTLD 1W2BD 1S72D 1Q81F 3G6ED 3OW2D 4WCED 2OGKA 3CCQD 1VQ8D 1VQOD 4IOCD 3D7AA 1QVGD 2ZJPD 1MJIA 5H1SH 1YITD 2WNYA 3PIOD 3DLLD 3G4SD 3CMAD 5GAGF 1Q7YF 2PZZA 3C9GA 4WFND 1M1KF 1VQKD 1YHQD 1YIJD 1VQ7D 4WF9D 3CC4D 2QA4D 3CC2D 1Q82F 1KD1F 3CD6D 4IOAD 2ZJRD 5GAEF 3I55D 5DM7D 3PIPD 2QEXD 1VQ4D 1VQ6D 2NWUA 1YI2D 1KC8F 3CPWD 3CF5D 1VQLD 3CCMD 5GAHF 1NJIF 1K8AF 5JVGD 1Q86F 5GADF 4WFBD 3CMED 3CCED 1YJWD 4UY8F 1VQND 2NRQA 3CXCD 1M90F 1VQMD 1VQ9D 2ZJQD 1YJND 1N8RF 5DM6D 1K9MF 3CCSD 1YJ9D 3CCUD 3G71D 4WFAD 5HL7D 3CCLD 1K73F 5MLCG 1VQPD 1QVFD 3CCVD 1JJ2D 4IO9D 2OTJD 1VQ5D 1KQSD 3CCRD 3J7ZF 3I56D 5JVHD 1IQ4A
chains in the Genus database with same CATH superfamily
3CCJD 4U67D 3CC7D 2OTLD 1W2BD 1S72D 1Q81F 3G6ED 3OW2D 4WCED 2OGKA 3CCQD 1VQ8D 1VQOD 4IOCD 3D7AA 1QVGD 2ZJPD 1MJIA 5H1SH 1YITD 2WNYA 3PIOD 3DLLD 3G4SD 3CMAD 5GAGF 1Q7YF 2PZZA 3C9GA 4WFND 1M1KF 1VQKD 1YHQD 1YIJD 1VQ7D 4WF9D 3CC4D 2QA4D 3CC2D 1Q82F 1KD1F 3CD6D 4IOAD 2ZJRD 5GAEF 3I55D 5DM7D 3PIPD 2QEXD 1VQ4D 1VQ6D 2NWUA 1YI2D 1KC8F 3CPWD 3CF5D 1VQLD 3CCMD 5GAHF 1NJIF 1K8AF 5JVGD 1Q86F 5GADF 4WFBD 3CMED 3CCED 1YJWD 4UY8F 1VQND 2NRQA 3CXCD 1M90F 1VQMD 1VQ9D 2ZJQD 1YJND 1N8RF 5DM6D 1K9MF 3CCSD 1YJ9D 3CCUD 3G71D 4WFAD 5HL7D 3CCLD 1K73F 5MLCG 1VQPD 1QVFD 3CCVD 1JJ2D 4IO9D 2OTJD 1VQ5D 1KQSD 3CCRD 3J7ZF 3I56D 5JVHD 1IQ4A
chains in the Genus database with same CATH topology
3CCJD 4U67D 3CC7D 2OTLD 1W2BD 1S72D 1Q81F 3G6ED 3OW2D 4WCED 2OGKA 3CCQD 1VQ8D 1VQOD 4IOCD 3D7AA 1QVGD 2ZJPD 1MJIA 5H1SH 1YITD 2WNYA 3PIOD 3DLLD 3G4SD 3CMAD 5GAGF 1Q7YF 2PZZA 3C9GA 4WFND 1M1KF 1VQKD 1YHQD 1YIJD 1VQ7D 4WF9D 3CC4D 2QA4D 3CC2D 1Q82F 1KD1F 3CD6D 4IOAD 2ZJRD 5GAEF 3I55D 5DM7D 3PIPD 2QEXD 1VQ4D 1VQ6D 2NWUA 1YI2D 1KC8F 3CPWD 3CF5D 1VQLD 3CCMD 5GAHF 1NJIF 1K8AF 5JVGD 1Q86F 5GADF 4WFBD 3CMED 3CCED 1YJWD 4UY8F 1VQND 2NRQA 3CXCD 1M90F 1VQMD 1VQ9D 2ZJQD 1YJND 1N8RF 5DM6D 1K9MF 3CCSD 1YJ9D 3CCUD 3G71D 4WFAD 5HL7D 3CCLD 1K73F 5MLCG 1VQPD 1QVFD 3CCVD 1JJ2D 4IO9D 2OTJD 1VQ5D 1KQSD 3CCRD 3J7ZF 3I56D 5JVHD 1IQ4A
chains in the Genus database with same CATH homology


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