4GKJR

Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human mitochondrial anticodon stem loop (asl) of transfer rna methionine (trnamet) bound to an mrna with an aug-codon in the a-site and paromomycin.
Total Genus 22
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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
22
sequence length
73
structure length
73
Chain Sequence
PSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRARILGLLPFTEKLVRK
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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 Expanded use of sense codons is regulated by modified cytidines in tRNA.
pubmed doi rcsb
molecule tags Ribosome/antibiotic
molecule keywords 16S rRNA
total genus 22
structure length 73
sequence length 73
ec nomenclature
pdb deposition date 2012-08-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
R PF01084 Ribosomal_S18 Ribosomal protein S18
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
4.10.640.10 Few Secondary Structures Irregular 30s Ribosomal Protein S18 Ribosomal protein S18 4gkjR00
4DV7R 2UUCR 3T1YR 4DUYR 5BR8R 4LF4R 4DR2R 4B3RR 4JI2R 4AQYR 4LFAR 5LMUR 4X65R 4DV0R 1IBLR 2VQFR 2UXDR 1N33R 4LF6R 4X64R 4JI7R 4X66R 1N32R 1XMOR 4LFBR 5LMNR 4OX9R 1HNZR 1FJGR 4LFCR 4YHHR 1I94R 4DR7R 1HNXR 4DV3R 4K0KR 1XNQR 4JI8R 1G1XC 4DR6R 1IBMR 4LF7R 4DR5R 4LF9R 4NXNR 4JI4R 4B3MR 4JI6R 1XNRR 4GKKR 4JV5R 2UUBR 4LF5R 4JI3R 4DR3R 3OTOR 1HR0R 4KHPR 1XMQR 4DR4R 4JYAR 4B3SR 4YY3R 4LF8R 1HNWR 4DV6R 4B3TR 4DV2R 4DR1R 2UXBR 2UU9R 1N34R 4JI5R 2E5LR 4JI1R 4NXMR 2UXCR 4DV4R 4X62R 2HHHR 1IBKR 2UUAR 1FKAR 2ZM6R 4DUZR 4JI0R 1N36R 4DV5R 2VQER 1J5ER 4DV1R 3T1HR 4GKJR 2F4VR
chains in the Genus database with same CATH superfamily
4DV7R 2UUCR 3T1YR 4DUYR 5BR8R 4LF4R 4DR2R 4B3RR 4JI2R 4AQYR 4LFAR 5LMUR 4X65R 4DV0R 1IBLR 2VQFR 2UXDR 1N33R 4LF6R 4X64R 4JI7R 4X66R 1N32R 1XMOR 4LFBR 5LMNR 4OX9R 1HNZR 1FJGR 4LFCR 4YHHR 1I94R 4DR7R 1HNXR 4DV3R 4K0KR 1XNQR 4JI8R 1G1XC 4DR6R 1IBMR 4LF7R 4DR5R 4LF9R 4NXNR 4JI4R 4B3MR 4JI6R 1XNRR 4GKKR 4JV5R 2UUBR 4LF5R 4JI3R 4DR3R 3OTOR 1HR0R 4KHPR 1XMQR 4DR4R 4JYAR 4B3SR 4YY3R 4LF8R 1HNWR 4DV6R 4B3TR 4DV2R 4DR1R 2UXBR 2UU9R 1N34R 4JI5R 2E5LR 4JI1R 4NXMR 2UXCR 4DV4R 4X62R 2HHHR 1IBKR 2UUAR 1FKAR 2ZM6R 4DUZR 4JI0R 1N36R 4DV5R 2VQER 1J5ER 4DV1R 3T1HR 4GKJR 2F4VR
chains in the Genus database with same CATH topology
4DV7R 2UUCR 3T1YR 4DUYR 5BR8R 4LF4R 4DR2R 4B3RR 4JI2R 4AQYR 4LFAR 5LMUR 4X65R 4DV0R 1IBLR 2VQFR 2UXDR 1N33R 4LF6R 4X64R 4JI7R 4X66R 1N32R 1XMOR 4LFBR 5LMNR 4OX9R 1HNZR 1FJGR 4LFCR 4YHHR 1I94R 4DR7R 1HNXR 4DV3R 4K0KR 1XNQR 4JI8R 1G1XC 4DR6R 1IBMR 4LF7R 4DR5R 4LF9R 4NXNR 4JI4R 4B3MR 4JI6R 1XNRR 4GKKR 4JV5R 2UUBR 4LF5R 4JI3R 4DR3R 3OTOR 1HR0R 4KHPR 1XMQR 4DR4R 4JYAR 4B3SR 4YY3R 4LF8R 1HNWR 4DV6R 4B3TR 4DV2R 4DR1R 2UXBR 2UU9R 1N34R 4JI5R 2E5LR 4JI1R 4NXMR 2UXCR 4DV4R 4X62R 2HHHR 1IBKR 2UUAR 1FKAR 2ZM6R 4DUZR 4JI0R 1N36R 4DV5R 2VQER 1J5ER 4DV1R 3T1HR 4GKJR 2F4VR
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4DV7 R;  2UUC R;  3T1Y R;  4DUY R;  5BR8 R;  4LF4 R;  4DR2 R;  4B3R R;  4JI2 R;  4AQY R;  4LFA R;  5LMU R;  4X65 R;  4DV0 R;  1IBL R;  2VQF R;  2UXD R;  1N33 R;  4LF6 R;  4X64 R;  4JI7 R;  4X66 R;  1N32 R;  1XMO R;  4LFB R;  5LMN R;  4OX9 R;  1HNZ R;  1FJG R;  4LFC R;  4YHH R;  1I94 R;  4DR7 R;  1HNX R;  4DV3 R;  4K0K R;  1XNQ R;  4JI8 R;  1G1X C;  4DR6 R;  1IBM R;  4LF7 R;  4DR5 R;  4LF9 R;  4NXN R;  4JI4 R;  4B3M R;  4JI6 R;  1XNR R;  4GKK R;  4JV5 R;  2UUB R;  4LF5 R;  4JI3 R;  4DR3 R;  3OTO R;  1HR0 R;  4KHP R;  1XMQ R;  4DR4 R;  4JYA R;  4B3S R;  4YY3 R;  4LF8 R;  1HNW R;  4DV6 R;  4B3T R;  4DV2 R;  4DR1 R;  2UXB R;  2UU9 R;  1N34 R;  4JI5 R;  2E5L R;  4JI1 R;  4NXM R;  2UXC R;  4DV4 R;  4X62 R;  2HHH R;  1IBK R;  2UUA R;  1FKA R;  2ZM6 R;  4DUZ R;  4JI0 R;  1N36 R;  4DV5 R;  2VQE R;  1J5E R;  4DV1 R;  3T1H R;  4GKJ R;  2F4V R; 
#chains in the Genus database with same CATH topology
 4DV7 R;  2UUC R;  3T1Y R;  4DUY R;  5BR8 R;  4LF4 R;  4DR2 R;  4B3R R;  4JI2 R;  4AQY R;  4LFA R;  5LMU R;  4X65 R;  4DV0 R;  1IBL R;  2VQF R;  2UXD R;  1N33 R;  4LF6 R;  4X64 R;  4JI7 R;  4X66 R;  1N32 R;  1XMO R;  4LFB R;  5LMN R;  4OX9 R;  1HNZ R;  1FJG R;  4LFC R;  4YHH R;  1I94 R;  4DR7 R;  1HNX R;  4DV3 R;  4K0K R;  1XNQ R;  4JI8 R;  1G1X C;  4DR6 R;  1IBM R;  4LF7 R;  4DR5 R;  4LF9 R;  4NXN R;  4JI4 R;  4B3M R;  4JI6 R;  1XNR R;  4GKK R;  4JV5 R;  2UUB R;  4LF5 R;  4JI3 R;  4DR3 R;  3OTO R;  1HR0 R;  4KHP R;  1XMQ R;  4DR4 R;  4JYA R;  4B3S R;  4YY3 R;  4LF8 R;  1HNW R;  4DV6 R;  4B3T R;  4DV2 R;  4DR1 R;  2UXB R;  2UU9 R;  1N34 R;  4JI5 R;  2E5L R;  4JI1 R;  4NXM R;  2UXC R;  4DV4 R;  4X62 R;  2HHH R;  1IBK R;  2UUA R;  1FKA R;  2ZM6 R;  4DUZ R;  4JI0 R;  1N36 R;  4DV5 R;  2VQE R;  1J5E R;  4DV1 R;  3T1H R;  4GKJ R;  2F4V R; 
#chains in the Genus database with same CATH homology
 4DV7 R;  2UUC R;  3T1Y R;  4DUY R;  5BR8 R;  4LF4 R;  4DR2 R;  4B3R R;  4JI2 R;  4AQY R;  4LFA R;  5LMU R;  4X65 R;  4DV0 R;  1IBL R;  2VQF R;  2UXD R;  1N33 R;  4LF6 R;  4X64 R;  4JI7 R;  4X66 R;  1N32 R;  1XMO R;  4LFB R;  5LMN R;  4OX9 R;  1HNZ R;  1FJG R;  4LFC R;  4YHH R;  1I94 R;  4DR7 R;  1HNX R;  4DV3 R;  4K0K R;  1XNQ R;  4JI8 R;  1G1X C;  4DR6 R;  1IBM R;  4LF7 R;  4DR5 R;  4LF9 R;  4NXN R;  4JI4 R;  4B3M R;  4JI6 R;  1XNR R;  4GKK R;  4JV5 R;  2UUB R;  4LF5 R;  4JI3 R;  4DR3 R;  3OTO R;  1HR0 R;  4KHP R;  1XMQ R;  4DR4 R;  4JYA R;  4B3S R;  4YY3 R;  4LF8 R;  1HNW R;  4DV6 R;  4B3T R;  4DV2 R;  4DR1 R;  2UXB R;  2UU9 R;  1N34 R;  4JI5 R;  2E5L R;  4JI1 R;  4NXM R;  2UXC R;  4DV4 R;  4X62 R;  2HHH R;  1IBK R;  2UUA R;  1FKA R;  2ZM6 R;  4DUZ R;  4JI0 R;  1N36 R;  4DV5 R;  2VQE R;  1J5E R;  4DV1 R;  3T1H R;  4GKJ R;  2F4V R; 
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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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