1VQ8D

The structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui
Total Genus 17
Loading diagram...

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
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
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, 1vq8D00
1KC8F 3CMAD 4WFAD 1MJIA 3CC7D 1QVFD 2ZJQD 3CF5D 3CCRD 5HL7D 3I56D 2WNYA 1VQPD 3CD6D 2NRQA 2ZJRD 3G6ED 1VQMD 3CCJD 4IO9D 1VQ9D 1KD1F 1Q82F 1JJ2D 2QEXD 1YJND 3CCED 3CMED 1Q81F 3CCMD 1VQKD 4WF9D 2OGKA 1M1KF 1YJWD 5JVHD 3CCQD 4IOCD 1IQ4A 3DLLD 1Q7YF 3PIOD 3G4SD 1VQLD 2ZJPD 5GAHF 1VQOD 1NJIF 3CCLD 1K8AF 1W2BD 1VQ4D 5H1SH 1KQSD 4U67D 4WCED 1VQ7D 3CCVD 4UY8F 3CC2D 3CCUD 1VQND 3CPWD 1VQ6D 5GAEF 1VQ8D 5JVGD 3G71D 1YIJD 4WFND 5DM7D 2QA4D 1YJ9D 1K73F 3I55D 3CXCD 4IOAD 1S72D 3CCSD 3D7AA 1QVGD 3C9GA 1K9MF 4WFBD 2PZZA 1Q86F 3J7ZF 2NWUA 5GAGF 3OW2D 2OTLD 1YHQD 1VQ5D 1YI2D 2OTJD 3PIPD 1M90F 3CC4D 1N8RF 5MLCG 5GADF 1YITD 5DM6D
chains in the Genus database with same CATH superfamily
1KC8F 3CMAD 4WFAD 1MJIA 3CC7D 1QVFD 2ZJQD 3CF5D 3CCRD 5HL7D 3I56D 2WNYA 1VQPD 3CD6D 2NRQA 2ZJRD 3G6ED 1VQMD 3CCJD 4IO9D 1VQ9D 1KD1F 1Q82F 1JJ2D 2QEXD 1YJND 3CCED 3CMED 1Q81F 3CCMD 1VQKD 4WF9D 2OGKA 1M1KF 1YJWD 5JVHD 3CCQD 4IOCD 1IQ4A 3DLLD 1Q7YF 3PIOD 3G4SD 1VQLD 2ZJPD 5GAHF 1VQOD 1NJIF 3CCLD 1K8AF 1W2BD 1VQ4D 5H1SH 1KQSD 4U67D 4WCED 1VQ7D 3CCVD 4UY8F 3CC2D 3CCUD 1VQND 3CPWD 1VQ6D 5GAEF 1VQ8D 5JVGD 3G71D 1YIJD 4WFND 5DM7D 2QA4D 1YJ9D 1K73F 3I55D 3CXCD 4IOAD 1S72D 3CCSD 3D7AA 1QVGD 3C9GA 1K9MF 4WFBD 2PZZA 1Q86F 3J7ZF 2NWUA 5GAGF 3OW2D 2OTLD 1YHQD 1VQ5D 1YI2D 2OTJD 3PIPD 1M90F 3CC4D 1N8RF 5MLCG 5GADF 1YITD 5DM6D
chains in the Genus database with same CATH topology
1KC8F 3CMAD 4WFAD 1MJIA 3CC7D 1QVFD 2ZJQD 3CF5D 3CCRD 5HL7D 3I56D 2WNYA 1VQPD 3CD6D 2NRQA 2ZJRD 3G6ED 1VQMD 3CCJD 4IO9D 1VQ9D 1KD1F 1Q82F 1JJ2D 2QEXD 1YJND 3CCED 3CMED 1Q81F 3CCMD 1VQKD 4WF9D 2OGKA 1M1KF 1YJWD 5JVHD 3CCQD 4IOCD 1IQ4A 3DLLD 1Q7YF 3PIOD 3G4SD 1VQLD 2ZJPD 5GAHF 1VQOD 1NJIF 3CCLD 1K8AF 1W2BD 1VQ4D 5H1SH 1KQSD 4U67D 4WCED 1VQ7D 3CCVD 4UY8F 3CC2D 3CCUD 1VQND 3CPWD 1VQ6D 5GAEF 1VQ8D 5JVGD 3G71D 1YIJD 4WFND 5DM7D 2QA4D 1YJ9D 1K73F 3I55D 3CXCD 4IOAD 1S72D 3CCSD 3D7AA 1QVGD 3C9GA 1K9MF 4WFBD 2PZZA 1Q86F 3J7ZF 2NWUA 5GAGF 3OW2D 2OTLD 1YHQD 1VQ5D 1YI2D 2OTJD 3PIPD 1M90F 3CC4D 1N8RF 5MLCG 5GADF 1YITD 5DM6D
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...