1YIT2

Crystal structure of virginiamycin m and s bound to the 50s ribosomal subunit of haloarcula marismortui
Total Genus 9
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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
9
sequence length
49
structure length
46
Chain Sequence
GKKSKATKKRLAKLDNQNSRVPAWVMLKTDRRNHKRRHWRRNDTDE
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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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publication title Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance.
pubmed doi rcsb
molecule tags Ribosome/antibiotic
molecule keywords 23S RIBOSOMAL RNA
total genus 9
structure length 46
sequence length 49
ec nomenclature
pdb deposition date 2005-01-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
2 PF00832 Ribosomal_L39 Ribosomal L39 protein
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1620.10 Mainly Alpha Orthogonal Bundle Atp Synthase Epsilon Chain; Chain: I; Ribosomal protein L39e 1yit200
3CCL2 1VQ62 1VQM2 1YJ92 1M903 3CD62 1K733 3CME2 3I562 3OW21 1VQ42 1KD13 1VQK2 3G4S2 1KC83 3CCR2 3CPW1 1YI22 1K9M3 2OTJ2 3CCM2 1Q823 1Q863 3CCU2 3I552 1YHQ2 1S722 2OTL2 1VQ52 2QEX2 3CXC1 1K8A3 3CMA2 1JJ21 1M1K3 1QVG1 1QVF1 1YJN2 3CC22 3G6E2 1VQ82 3CCJ2 1YIT2 1VQO2 1Q813 3CC42 1VQP2 1VQ92 3CCQ2 1YIJ2 1VQN2 1VQL2 3CC72 3CCE2 1W2B1 1Q7Y3 1YJW2 1N8R3 3CCV2 1KQS1 1NJI3 2QA42 3CCS2 1VQ72 3G712
chains in the Genus database with same CATH superfamily
3CCL2 1VQ62 1VQM2 1YJ92 2WSSI 1M903 3CD62 1K733 3CME2 3I562 3OW21 1VQ42 1KD13 1VQK2 3OFNI 3G4S2 1KC83 3CCR2 3CPW1 4YXWI 1YI22 1K9M3 2OTJ2 3CCM2 1Q823 1Q863 3CCU2 3I552 1YHQ2 1S722 2OTL2 1VQ52 2QEX2 3ZIAI 3CXC1 2XNDI 1K8A3 3CMA2 1JJ21 1M1K3 1QVG1 2V7QI 1QVF1 1YJN2 3CC22 3G6E2 1VQ82 3CCJ2 1YIT2 1VQO2 1Q813 3CC42 1VQP2 1VQ92 3CCQ2 1YIJ2 2XOKI 1VQN2 1VQL2 3CC72 3CCE2 1W2B1 1Q7Y3 1YJW2 1N8R3 3CCV2 1KQS1 2WPDI 1NJI3 2QA42 1E79I 3CCS2 1VQ72 3G712
chains in the Genus database with same CATH topology
3CCL2 1VQ62 1VQM2 1YJ92 1M903 3CD62 1K733 3CME2 3I562 3OW21 1VQ42 1KD13 1VQK2 3G4S2 1KC83 3CCR2 3CPW1 1YI22 1K9M3 2OTJ2 3CCM2 1Q823 1Q863 3CCU2 3I552 1YHQ2 1S722 2OTL2 1VQ52 2QEX2 3CXC1 1K8A3 3CMA2 1JJ21 1M1K3 1QVG1 1QVF1 1YJN2 3CC22 3G6E2 1VQ82 3CCJ2 1YIT2 1VQO2 1Q813 3CC42 1VQP2 1VQ92 3CCQ2 1YIJ2 1VQN2 1VQL2 3CC72 3CCE2 1W2B1 1Q7Y3 1YJW2 1N8R3 3CCV2 1KQS1 1NJI3 2QA42 3CCS2 1VQ72 3G712
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3CCL 2;  1VQ6 2;  1VQM 2;  1YJ9 2;  1M90 3;  3CD6 2;  1K73 3;  3CME 2;  3I56 2;  3OW2 1;  1VQ4 2;  1KD1 3;  1VQK 2;  3G4S 2;  1KC8 3;  3CCR 2;  3CPW 1;  1YI2 2;  1K9M 3;  2OTJ 2;  3CCM 2;  1Q82 3;  1Q86 3;  3CCU 2;  3I55 2;  1YHQ 2;  1S72 2;  2OTL 2;  1VQ5 2;  2QEX 2;  3CXC 1;  1K8A 3;  3CMA 2;  1JJ2 1;  1M1K 3;  1QVG 1;  1QVF 1;  1YJN 2;  3CC2 2;  3G6E 2;  1VQ8 2;  3CCJ 2;  1YIT 2;  1VQO 2;  1Q81 3;  3CC4 2;  1VQP 2;  1VQ9 2;  3CCQ 2;  1YIJ 2;  1VQN 2;  1VQL 2;  3CC7 2;  3CCE 2;  1W2B 1;  1Q7Y 3;  1YJW 2;  1N8R 3;  3CCV 2;  1KQS 1;  1NJI 3;  2QA4 2;  3CCS 2;  1VQ7 2;  3G71 2; 
#chains in the Genus database with same CATH topology
 3CCL 2;  1VQ6 2;  1VQM 2;  1YJ9 2;  2WSS I;  1M90 3;  3CD6 2;  1K73 3;  3CME 2;  3I56 2;  3OW2 1;  1VQ4 2;  1KD1 3;  1VQK 2;  3OFN I;  3G4S 2;  1KC8 3;  3CCR 2;  3CPW 1;  4YXW I;  1YI2 2;  1K9M 3;  2OTJ 2;  3CCM 2;  1Q82 3;  1Q86 3;  3CCU 2;  3I55 2;  1YHQ 2;  1S72 2;  2OTL 2;  1VQ5 2;  2QEX 2;  3ZIA I;  3CXC 1;  2XND I;  1K8A 3;  3CMA 2;  1JJ2 1;  1M1K 3;  1QVG 1;  2V7Q I;  1QVF 1;  1YJN 2;  3CC2 2;  3G6E 2;  1VQ8 2;  3CCJ 2;  1YIT 2;  1VQO 2;  1Q81 3;  3CC4 2;  1VQP 2;  1VQ9 2;  3CCQ 2;  1YIJ 2;  2XOK I;  1VQN 2;  1VQL 2;  3CC7 2;  3CCE 2;  1W2B 1;  1Q7Y 3;  1YJW 2;  1N8R 3;  3CCV 2;  1KQS 1;  2WPD I;  1NJI 3;  2QA4 2;  1E79 I;  3CCS 2;  1VQ7 2;  3G71 2; 
#chains in the Genus database with same CATH homology
 3CCL 2;  1VQ6 2;  1VQM 2;  1YJ9 2;  1M90 3;  3CD6 2;  1K73 3;  3CME 2;  3I56 2;  3OW2 1;  1VQ4 2;  1KD1 3;  1VQK 2;  3G4S 2;  1KC8 3;  3CCR 2;  3CPW 1;  1YI2 2;  1K9M 3;  2OTJ 2;  3CCM 2;  1Q82 3;  1Q86 3;  3CCU 2;  3I55 2;  1YHQ 2;  1S72 2;  2OTL 2;  1VQ5 2;  2QEX 2;  3CXC 1;  1K8A 3;  3CMA 2;  1JJ2 1;  1M1K 3;  1QVG 1;  1QVF 1;  1YJN 2;  3CC2 2;  3G6E 2;  1VQ8 2;  3CCJ 2;  1YIT 2;  1VQO 2;  1Q81 3;  3CC4 2;  1VQP 2;  1VQ9 2;  3CCQ 2;  1YIJ 2;  1VQN 2;  1VQL 2;  3CC7 2;  3CCE 2;  1W2B 1;  1Q7Y 3;  1YJW 2;  1N8R 3;  3CCV 2;  1KQS 1;  1NJI 3;  2QA4 2;  3CCS 2;  1VQ7 2;  3G71 2; 
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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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