1JJ2D

Fully refined crystal structure of the haloarcula marismortui large ribosomal subunit at 2.4 angstrom resolution
Total Genus 16
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
16
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 RRNA
publication title The kink-turn: a new RNA secondary structure motif.
pubmed doi rcsb
total genus 16
structure length 140
sequence length 165
ec nomenclature
pdb deposition date 2001-07-03

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, 1jj2D00
1YHQD 1YJND 3CCJD 4WF9D 2QEXD 1YI2D 1VQLD 3G6ED 3CC2D 4IOAD 5JVHD 1KD1F 1VQKD 1Q82F 3I55D 1K73F 1QVGD 2ZJRD 4UY8F 3CCSD 2OGKA 1S72D 3CCRD 3CC7D 3CPWD 1YJWD 2PZZA 2OTLD 3CCLD 3I56D 1M1KF 3CCQD 1YJ9D 3CMED 1VQ6D 2ZJPD 3CD6D 5JVGD 1Q86F 1VQOD 1YIJD 1VQMD 5HL7D 1M90F 3G4SD 5H1SH 4WFBD 1KC8F 5MLCG 1VQ8D 3OW2D 2NRQA 1IQ4A 3CF5D 3CCVD 4IOCD 3D7AA 1VQ7D 3CCUD 1MJIA 1VQ5D 3CMAD 5DM7D 4IO9D 4WFAD 4U67D 1Q7YF 1VQ9D 2QA4D 1N8RF 1W2BD 5GAHF 1VQND 3G71D 5GADF 3J7ZF 5GAEF 5DM6D 1K9MF 3PIOD 1K8AF 1KQSD 3CXCD 1QVFD 2OTJD 1VQ4D 3CCED 3DLLD 4WCED 4WFND 1NJIF 2NWUA 2ZJQD 1Q81F 3CC4D 3C9GA 3PIPD 1VQPD 3CCMD 1YITD 1JJ2D 5GAGF 2WNYA
chains in the Genus database with same CATH superfamily
1YHQD 1YJND 3CCJD 4WF9D 2QEXD 1YI2D 1VQLD 3G6ED 3CC2D 4IOAD 5JVHD 1KD1F 1VQKD 1Q82F 3I55D 1K73F 1QVGD 2ZJRD 4UY8F 3CCSD 2OGKA 1S72D 3CCRD 3CC7D 3CPWD 1YJWD 2PZZA 2OTLD 3CCLD 3I56D 1M1KF 3CCQD 1YJ9D 3CMED 1VQ6D 2ZJPD 3CD6D 5JVGD 1Q86F 1VQOD 1YIJD 1VQMD 5HL7D 1M90F 3G4SD 5H1SH 4WFBD 1KC8F 5MLCG 1VQ8D 3OW2D 2NRQA 1IQ4A 3CF5D 3CCVD 4IOCD 3D7AA 1VQ7D 3CCUD 1MJIA 1VQ5D 3CMAD 5DM7D 4IO9D 4WFAD 4U67D 1Q7YF 1VQ9D 2QA4D 1N8RF 1W2BD 5GAHF 1VQND 3G71D 5GADF 3J7ZF 5GAEF 5DM6D 1K9MF 3PIOD 1K8AF 1KQSD 3CXCD 1QVFD 2OTJD 1VQ4D 3CCED 3DLLD 4WCED 4WFND 1NJIF 2NWUA 2ZJQD 1Q81F 3CC4D 3C9GA 3PIPD 1VQPD 3CCMD 1YITD 1JJ2D 5GAGF 2WNYA
chains in the Genus database with same CATH topology
1YHQD 1YJND 3CCJD 4WF9D 2QEXD 1YI2D 1VQLD 3G6ED 3CC2D 4IOAD 5JVHD 1KD1F 1VQKD 1Q82F 3I55D 1K73F 1QVGD 2ZJRD 4UY8F 3CCSD 2OGKA 1S72D 3CCRD 3CC7D 3CPWD 1YJWD 2PZZA 2OTLD 3CCLD 3I56D 1M1KF 3CCQD 1YJ9D 3CMED 1VQ6D 2ZJPD 3CD6D 5JVGD 1Q86F 1VQOD 1YIJD 1VQMD 5HL7D 1M90F 3G4SD 5H1SH 4WFBD 1KC8F 5MLCG 1VQ8D 3OW2D 2NRQA 1IQ4A 3CF5D 3CCVD 4IOCD 3D7AA 1VQ7D 3CCUD 1MJIA 1VQ5D 3CMAD 5DM7D 4IO9D 4WFAD 4U67D 1Q7YF 1VQ9D 2QA4D 1N8RF 1W2BD 5GAHF 1VQND 3G71D 5GADF 3J7ZF 5GAEF 5DM6D 1K9MF 3PIOD 1K8AF 1KQSD 3CXCD 1QVFD 2OTJD 1VQ4D 3CCED 3DLLD 4WCED 4WFND 1NJIF 2NWUA 2ZJQD 1Q81F 3CC4D 3C9GA 3PIPD 1VQPD 3CCMD 1YITD 1JJ2D 5GAGF 2WNYA
chains in the Genus database with same CATH homology


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