1VQLD

The structure of the transition state analogue "dcsn" bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 16
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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
16
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 16
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, 1vqlD00
1Q7YF 5DM7D 3CF5D 4UY8F 1KC8F 3CCMD 3CCQD 2OTLD 2NWUA 3CC7D 1VQ4D 4IOAD 5JVHD 3CCSD 1K8AF 1Q81F 3CMAD 4WCED 1NJIF 1N8RF 1K73F 3CCED 5GAHF 3G6ED 3CC2D 5GAGF 1KQSD 1VQ9D 3CD6D 3CCVD 1S72D 2NRQA 2ZJPD 1VQPD 1VQOD 1YJWD 3CC4D 5DM6D 2ZJQD 3DLLD 2QEXD 2OGKA 3PIOD 1VQ6D 2WNYA 4WFAD 4WFND 3J7ZF 2QA4D 4WFBD 3CPWD 1VQ7D 4U67D 3I56D 3CCLD 1K9MF 1M1KF 1QVFD 1YITD 1Q82F 1VQ5D 1YIJD 3CCRD 1QVGD 5HL7D 1YHQD 1VQ8D 3I55D 1YJND 1Q86F 3C9GA 3CMED 1JJ2D 3CCUD 1IQ4A 4IOCD 5JVGD 2OTJD 4IO9D 5MLCG 3CXCD 3CCJD 3G4SD 1W2BD 1VQKD 1M90F 5GADF 1KD1F 2ZJRD 1MJIA 3PIPD 1YJ9D 3G71D 1VQLD 1VQND 5GAEF 3OW2D 1VQMD 2PZZA 4WF9D 3D7AA 5H1SH 1YI2D
chains in the Genus database with same CATH superfamily
1Q7YF 5DM7D 3CF5D 4UY8F 1KC8F 3CCMD 3CCQD 2OTLD 2NWUA 3CC7D 1VQ4D 4IOAD 5JVHD 3CCSD 1K8AF 1Q81F 3CMAD 4WCED 1NJIF 1N8RF 1K73F 3CCED 5GAHF 3G6ED 3CC2D 5GAGF 1KQSD 1VQ9D 3CD6D 3CCVD 1S72D 2NRQA 2ZJPD 1VQPD 1VQOD 1YJWD 3CC4D 5DM6D 2ZJQD 3DLLD 2QEXD 2OGKA 3PIOD 1VQ6D 2WNYA 4WFAD 4WFND 3J7ZF 2QA4D 4WFBD 3CPWD 1VQ7D 4U67D 3I56D 3CCLD 1K9MF 1M1KF 1QVFD 1YITD 1Q82F 1VQ5D 1YIJD 3CCRD 1QVGD 5HL7D 1YHQD 1VQ8D 3I55D 1YJND 1Q86F 3C9GA 3CMED 1JJ2D 3CCUD 1IQ4A 4IOCD 5JVGD 2OTJD 4IO9D 5MLCG 3CXCD 3CCJD 3G4SD 1W2BD 1VQKD 1M90F 5GADF 1KD1F 2ZJRD 1MJIA 3PIPD 1YJ9D 3G71D 1VQLD 1VQND 5GAEF 3OW2D 1VQMD 2PZZA 4WF9D 3D7AA 5H1SH 1YI2D
chains in the Genus database with same CATH topology
1Q7YF 5DM7D 3CF5D 4UY8F 1KC8F 3CCMD 3CCQD 2OTLD 2NWUA 3CC7D 1VQ4D 4IOAD 5JVHD 3CCSD 1K8AF 1Q81F 3CMAD 4WCED 1NJIF 1N8RF 1K73F 3CCED 5GAHF 3G6ED 3CC2D 5GAGF 1KQSD 1VQ9D 3CD6D 3CCVD 1S72D 2NRQA 2ZJPD 1VQPD 1VQOD 1YJWD 3CC4D 5DM6D 2ZJQD 3DLLD 2QEXD 2OGKA 3PIOD 1VQ6D 2WNYA 4WFAD 4WFND 3J7ZF 2QA4D 4WFBD 3CPWD 1VQ7D 4U67D 3I56D 3CCLD 1K9MF 1M1KF 1QVFD 1YITD 1Q82F 1VQ5D 1YIJD 3CCRD 1QVGD 5HL7D 1YHQD 1VQ8D 3I55D 1YJND 1Q86F 3C9GA 3CMED 1JJ2D 3CCUD 1IQ4A 4IOCD 5JVGD 2OTJD 4IO9D 5MLCG 3CXCD 3CCJD 3G4SD 1W2BD 1VQKD 1M90F 5GADF 1KD1F 2ZJRD 1MJIA 3PIPD 1YJ9D 3G71D 1VQLD 1VQND 5GAEF 3OW2D 1VQMD 2PZZA 4WF9D 3D7AA 5H1SH 1YI2D
chains in the Genus database with same CATH homology


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