4GKJD

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 54
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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
54
sequence length
208
structure length
208
Chain Sequence
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR
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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.


  Genus data interpretation
Chord Diagram
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connected with : NaN
molecule tags Ribosome/antibiotic
publication title Expanded use of sense codons is regulated by modified cytidines in tRNA.
pubmed doi rcsb
molecule keywords 16S rRNA
total genus 54
structure length 208
sequence length 208
ec nomenclature
pdb deposition date 2012-08-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
D PF00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain
D PF01479 S4 S4 domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41; Chain A, domain 1 Ribosomal Protein S4 Delta 41; Chain A, domain 1 4gkjD01
3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A RNA-binding S4 domain 4gkjD02
1N36D 1C05A 4DV0D 5LMUD 4JI8D 2UU9D 2E5LD 4NXMD 4DV5D 1IBLD 4JI0D 4LF5D 4LF9D 4JV5D 4DR1D 4X65D 1IBKD 4LFAD 4X66D 3T1HD 2K6PA 3HP7A 1H3FA 1XNQD 4DV1D 4GKKD 4DV3D 4K0KD 1N34D 4LF8D 2VQED 1JH3A 4DV4D 4JI2D 4OUDA 1HR0D 4DR6D 4YHHD 4JYAD 2UXCD 4LFBD 1FKAD 1XNRD 1VIOA 2VQFD 4B3SD 4AQYD 2ZM6D 4DV6D 4X62D 4DR4D 4OX9D 2UUCD 4JI1D 4DR7D 4LGTA 1C06A 1IBMD 2UUBD 4JI4D 4LFCD 2ISTA 4B3TD 1FJGD 2UXBD 1I94D 4B3RD 2UUAD 1H3EA 3KBGA 1KSKA 1HNXD 1HNWD 1KSVA 1P9KA 2KTLA 1N32D 4LF7D 4JI7D 5BR8D 4GKJD 4LF6D 4B3MD 3T1YD 4KHPD 4DR2D 3DH3A 4JI5D 4LF4D 5LMND 4JI3D 2HHHD 2F4VD 4JI6D 4NXND 4DV2D 1KSLA 4DV7D 1N33D 4DR5D 4DR3D 5IWAD 3OTOD 1HNZD 4DUZD 2UXDD 4DUYD 1XMOD 1DM9A 4YY3D 2JANA 4X64D 1J5ED 1XMQD
chains in the Genus database with same CATH superfamily
5FLXE 1N36D 1C05A 4DV0D 5LMUD 4JI8D 4II3A 2UU9D 2E5LD 4NXMD 4DV5D 1IBLD 4JI0D 5A2QE 4LF5D 4LF9D 4JV5D 4DR1D 4X65D 1IBKD 4LFAD 4X66D 3T1HD 2K6PA 3HP7A 1H3FA 1XNQD 4W5VB 4DV1D 4GKKD 2L3NA 4DV3D 4K0KD 1N34D 4LF8D 2VQED 1JH3A 4DV4D 2I1SA 4JI2D 4OUDA 1HR0D 4DR6D 4YHHD 4JYAD 2UXCD 4LFBD 1FKAD 1XNRD 1VIOA 3J7AF 2VQFD 4B3SD 4AQYD 2ZM6D 4DV6D 4NNJA 4II2A 4X62D 3KYDB 4DR4D 3KYCB 4OX9D 2UUCD 4JI1D 4DR7D 4LGTA 1C06A 1IBMD 2UUBD 1Y8XB 4JI4D 4LFCD 2ISTA 4B3TD 1FJGD 2UXBD 1I94D 3J81E 4B3RD 2UUAD 3JAME 1H3EA 3KBGA 5KNLA 1KSKA 1HNXD 1HNWD 1KSVA 1P9KA 2KTLA 1N32D 3CMMA 4LF7D 2ZTBA 4JI7D 5BR8D 3J80E 4GKJD 5FQ2B 4LF6D 4B3MD 3T1YD 4KHPD 4DR2D 3DH3A 4JI5D 4LF4D 5LMND 4JI3D 2HHHD 2F4VD 1Y8QB 4JI6D 4NXND 4DV2D 5IT9E 1KSLA 4DV7D 1N33D 3ONHA 4DR5D 4DR3D 5IWAD 3OTOD 1HNZD 2LQ7A 4DUZD 2UXDD 4DUYD 5LL6S 3ONGA 1Y8RB 1XMOD 1DM9A 4YY3D 3FN1A 2JANA 4X64D 2NVUB 1J5ED 1XMQD
chains in the Genus database with same CATH topology
1N36D 1C05A 4DV0D 5LMUD 4JI8D 2UU9D 2E5LD 4NXMD 4DV5D 1IBLD 4JI0D 4LF5D 4LF9D 4JV5D 4DR1D 4X65D 1IBKD 4LFAD 4X66D 3T1HD 2K6PA 3HP7A 1H3FA 1XNQD 4DV1D 4GKKD 2L3NA 4DV3D 4K0KD 1N34D 4LF8D 2VQED 1JH3A 4DV4D 4JI2D 4OUDA 1HR0D 4DR6D 4YHHD 4JYAD 2UXCD 4LFBD 1FKAD 1XNRD 1VIOA 2VQFD 4B3SD 4AQYD 2ZM6D 4DV6D 4X62D 4DR4D 4OX9D 2UUCD 4JI1D 4DR7D 4LGTA 1C06A 1IBMD 2UUBD 4JI4D 4LFCD 2ISTA 4B3TD 1FJGD 2UXBD 1I94D 4B3RD 2UUAD 1H3EA 3KBGA 1KSKA 1HNXD 1HNWD 1KSVA 1P9KA 2KTLA 1N32D 4LF7D 4JI7D 5BR8D 4GKJD 4LF6D 4B3MD 3T1YD 4KHPD 4DR2D 3DH3A 4JI5D 4LF4D 5LMND 4JI3D 2HHHD 2F4VD 4JI6D 4NXND 4DV2D 1KSLA 4DV7D 1N33D 4DR5D 4DR3D 5IWAD 3OTOD 1HNZD 4DUZD 2UXDD 4DUYD 1XMOD 1DM9A 4YY3D 2JANA 4X64D 1J5ED 1XMQD
chains in the Genus database with same CATH homology

  
#chains in the Genus database with same CATH superfamily
 1N36 D;  1C05 A;  4DV0 D;  5LMU D;  4JI8 D;  2UU9 D;  2E5L D;  4NXM D;  4DV5 D;  1IBL D;  4JI0 D;  4LF5 D;  4LF9 D;  4JV5 D;  4DR1 D;  4X65 D;  1IBK D;  4LFA D;  4X66 D;  3T1H D;  2K6P A;  3HP7 A;  1H3F A;  1XNQ D;  4DV1 D;  4GKK D;  4DV3 D;  4K0K D;  1N34 D;  4LF8 D;  2VQE D;  1JH3 A;  4DV4 D;  4JI2 D;  4OUD A;  1HR0 D;  4DR6 D;  4YHH D;  4JYA D;  2UXC D;  4LFB D;  1FKA D;  1XNR D;  1VIO A;  2VQF D;  4B3S D;  4AQY D;  2ZM6 D;  4DV6 D;  4X62 D;  4DR4 D;  4OX9 D;  2UUC D;  4JI1 D;  4DR7 D;  4LGT A;  1C06 A;  1IBM D;  2UUB D;  4JI4 D;  4LFC D;  2IST A;  4B3T D;  1FJG D;  2UXB D;  1I94 D;  4B3R D;  2UUA D;  1H3E A;  3KBG A;  1KSK A;  1HNX D;  1HNW D;  1KSV A;  1P9K A;  2KTL A;  1N32 D;  4LF7 D;  4JI7 D;  5BR8 D;  4GKJ D;  4LF6 D;  4B3M D;  3T1Y D;  4KHP D;  4DR2 D;  3DH3 A;  4JI5 D;  4LF4 D;  5LMN D;  4JI3 D;  2HHH D;  2F4V D;  4JI6 D;  4NXN D;  4DV2 D;  1KSL A;  4DV7 D;  1N33 D;  4DR5 D;  4DR3 D;  5IWA D;  3OTO D;  1HNZ D;  4DUZ D;  2UXD D;  4DUY D;  1XMO D;  1DM9 A;  4YY3 D;  2JAN A;  4X64 D;  1J5E D;  1XMQ D; 
#chains in the Genus database with same CATH topology
 5FLX E;  1N36 D;  1C05 A;  4DV0 D;  5LMU D;  4JI8 D;  4II3 A;  2UU9 D;  2E5L D;  4NXM D;  4DV5 D;  1IBL D;  4JI0 D;  5A2Q E;  4LF5 D;  4LF9 D;  4JV5 D;  4DR1 D;  4X65 D;  1IBK D;  4LFA D;  4X66 D;  3T1H D;  2K6P A;  3HP7 A;  1H3F A;  1XNQ D;  4W5V B;  4DV1 D;  4GKK D;  2L3N A;  4DV3 D;  4K0K D;  1N34 D;  4LF8 D;  2VQE D;  1JH3 A;  4DV4 D;  2I1S A;  4JI2 D;  4OUD A;  1HR0 D;  4DR6 D;  4YHH D;  4JYA D;  2UXC D;  4LFB D;  1FKA D;  1XNR D;  1VIO A;  3J7A F;  2VQF D;  4B3S D;  4AQY D;  2ZM6 D;  4DV6 D;  4NNJ A;  4II2 A;  4X62 D;  3KYD B;  4DR4 D;  3KYC B;  4OX9 D;  2UUC D;  4JI1 D;  4DR7 D;  4LGT A;  1C06 A;  1IBM D;  2UUB D;  1Y8X B;  4JI4 D;  4LFC D;  2IST A;  4B3T D;  1FJG D;  2UXB D;  1I94 D;  3J81 E;  4B3R D;  2UUA D;  3JAM E;  1H3E A;  3KBG A;  5KNL A;  1KSK A;  1HNX D;  1HNW D;  1KSV A;  1P9K A;  2KTL A;  1N32 D;  3CMM A;  4LF7 D;  2ZTB A;  4JI7 D;  5BR8 D;  3J80 E;  4GKJ D;  5FQ2 B;  4LF6 D;  4B3M D;  3T1Y D;  4KHP D;  4DR2 D;  3DH3 A;  4JI5 D;  4LF4 D;  5LMN D;  4JI3 D;  2HHH D;  2F4V D;  1Y8Q B;  4JI6 D;  4NXN D;  4DV2 D;  5IT9 E;  1KSL A;  4DV7 D;  1N33 D;  3ONH A;  4DR5 D;  4DR3 D;  5IWA D;  3OTO D;  1HNZ D;  2LQ7 A;  4DUZ D;  2UXD D;  4DUY D;  5LL6 S;  3ONG A;  1Y8R B;  1XMO D;  1DM9 A;  4YY3 D;  3FN1 A;  2JAN A;  4X64 D;  2NVU B;  1J5E D;  1XMQ D; 
#chains in the Genus database with same CATH homology
 1N36 D;  1C05 A;  4DV0 D;  5LMU D;  4JI8 D;  2UU9 D;  2E5L D;  4NXM D;  4DV5 D;  1IBL D;  4JI0 D;  4LF5 D;  4LF9 D;  4JV5 D;  4DR1 D;  4X65 D;  1IBK D;  4LFA D;  4X66 D;  3T1H D;  2K6P A;  3HP7 A;  1H3F A;  1XNQ D;  4DV1 D;  4GKK D;  2L3N A;  4DV3 D;  4K0K D;  1N34 D;  4LF8 D;  2VQE D;  1JH3 A;  4DV4 D;  4JI2 D;  4OUD A;  1HR0 D;  4DR6 D;  4YHH D;  4JYA D;  2UXC D;  4LFB D;  1FKA D;  1XNR D;  1VIO A;  2VQF D;  4B3S D;  4AQY D;  2ZM6 D;  4DV6 D;  4X62 D;  4DR4 D;  4OX9 D;  2UUC D;  4JI1 D;  4DR7 D;  4LGT A;  1C06 A;  1IBM D;  2UUB D;  4JI4 D;  4LFC D;  2IST A;  4B3T D;  1FJG D;  2UXB D;  1I94 D;  4B3R D;  2UUA D;  1H3E A;  3KBG A;  1KSK A;  1HNX D;  1HNW D;  1KSV A;  1P9K A;  2KTL A;  1N32 D;  4LF7 D;  4JI7 D;  5BR8 D;  4GKJ D;  4LF6 D;  4B3M D;  3T1Y D;  4KHP D;  4DR2 D;  3DH3 A;  4JI5 D;  4LF4 D;  5LMN D;  4JI3 D;  2HHH D;  2F4V D;  4JI6 D;  4NXN D;  4DV2 D;  1KSL A;  4DV7 D;  1N33 D;  4DR5 D;  4DR3 D;  5IWA D;  3OTO D;  1HNZ D;  4DUZ D;  2UXD D;  4DUY D;  1XMO D;  1DM9 A;  4YY3 D;  2JAN A;  4X64 D;  1J5E D;  1XMQ 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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