1VQMD

The structure of the transition state analogue "dan" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 17
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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
17
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 Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.
pubmed doi rcsb
total genus 17
structure length 140
sequence length 165
ec nomenclature
pdb deposition date 2004-12-16

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, 1vqmD00
1VQ8D 1VQOD 3CC7D 3OW2D 3CXCD 5JVGD 1Q7YF 5HL7D 3I55D 2NRQA 1YJ9D 3CCVD 1IQ4A 2PZZA 1YHQD 2OTJD 1VQMD 3J7ZF 1QVGD 1VQ6D 3CCQD 3CCED 1W2BD 1Q82F 1Q86F 3G4SD 1YIJD 1VQKD 5DM6D 3CCMD 1JJ2D 3CC2D 1VQLD 4WCED 3I56D 2ZJQD 2QEXD 5GAEF 3G71D 1K73F 2NWUA 3G6ED 1K9MF 1YJND 2QA4D 3DLLD 1K8AF 4WFBD 5JVHD 2ZJRD 1VQPD 1VQ5D 1S72D 1VQ9D 5GADF 1YI2D 5GAGF 3PIOD 2OTLD 3CCJD 1M1KF 1KD1F 4WF9D 3D7AA 1YITD 1KC8F 5DM7D 1VQ7D 1VQ4D 2ZJPD 2WNYA 3CMAD 1QVFD 5GAHF 4WFND 1NJIF 5MLCG 3CCSD 4IOAD 1N8RF 4UY8F 2OGKA 3PIPD 1YJWD 3CMED 4WFAD 3CCRD 4IOCD 1KQSD 5H1SH 3CCLD 1Q81F 1VQND 1MJIA 4U67D 3C9GA 3CC4D 1M90F 3CCUD 4IO9D 3CPWD 3CF5D 3CD6D
chains in the Genus database with same CATH superfamily
1VQ8D 1VQOD 3CC7D 3OW2D 3CXCD 5JVGD 1Q7YF 5HL7D 3I55D 2NRQA 1YJ9D 3CCVD 1IQ4A 2PZZA 1YHQD 2OTJD 1VQMD 3J7ZF 1QVGD 1VQ6D 3CCQD 3CCED 1W2BD 1Q82F 1Q86F 3G4SD 1YIJD 1VQKD 5DM6D 3CCMD 1JJ2D 3CC2D 1VQLD 4WCED 3I56D 2ZJQD 2QEXD 5GAEF 3G71D 1K73F 2NWUA 3G6ED 1K9MF 1YJND 2QA4D 3DLLD 1K8AF 4WFBD 5JVHD 2ZJRD 1VQPD 1VQ5D 1S72D 1VQ9D 5GADF 1YI2D 5GAGF 3PIOD 2OTLD 3CCJD 1M1KF 1KD1F 4WF9D 3D7AA 1YITD 1KC8F 5DM7D 1VQ7D 1VQ4D 2ZJPD 2WNYA 3CMAD 1QVFD 5GAHF 4WFND 1NJIF 5MLCG 3CCSD 4IOAD 1N8RF 4UY8F 2OGKA 3PIPD 1YJWD 3CMED 4WFAD 3CCRD 4IOCD 1KQSD 5H1SH 3CCLD 1Q81F 1VQND 1MJIA 4U67D 3C9GA 3CC4D 1M90F 3CCUD 4IO9D 3CPWD 3CF5D 3CD6D
chains in the Genus database with same CATH topology
1VQ8D 1VQOD 3CC7D 3OW2D 3CXCD 5JVGD 1Q7YF 5HL7D 3I55D 2NRQA 1YJ9D 3CCVD 1IQ4A 2PZZA 1YHQD 2OTJD 1VQMD 3J7ZF 1QVGD 1VQ6D 3CCQD 3CCED 1W2BD 1Q82F 1Q86F 3G4SD 1YIJD 1VQKD 5DM6D 3CCMD 1JJ2D 3CC2D 1VQLD 4WCED 3I56D 2ZJQD 2QEXD 5GAEF 3G71D 1K73F 2NWUA 3G6ED 1K9MF 1YJND 2QA4D 3DLLD 1K8AF 4WFBD 5JVHD 2ZJRD 1VQPD 1VQ5D 1S72D 1VQ9D 5GADF 1YI2D 5GAGF 3PIOD 2OTLD 3CCJD 1M1KF 1KD1F 4WF9D 3D7AA 1YITD 1KC8F 5DM7D 1VQ7D 1VQ4D 2ZJPD 2WNYA 3CMAD 1QVFD 5GAHF 4WFND 1NJIF 5MLCG 3CCSD 4IOAD 1N8RF 4UY8F 2OGKA 3PIPD 1YJWD 3CMED 4WFAD 3CCRD 4IOCD 1KQSD 5H1SH 3CCLD 1Q81F 1VQND 1MJIA 4U67D 3C9GA 3CC4D 1M90F 3CCUD 4IO9D 3CPWD 3CF5D 3CD6D
chains in the Genus database with same CATH homology


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