4K0KD

Crystal structure of the thermus thermophilus 30s ribosomal subunit complexed with a serine-asl and mrna containing a stop codon
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.

Chord Diagram
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molecule keywords 16S ribosomal RNA
publication title Unusual base pairing during the decoding of a stop codon by the ribosome.
pubmed doi rcsb
molecule tags Ribosome
total genus 54
structure length 208
sequence length 208
ec nomenclature
pdb deposition date 2013-04-04

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 4k0kD01
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 4k0kD02
5BR8D 2VQED 4X66D 3DH3A 1JH3A 1H3FA 5LMUD 2UXBD 5LMND 3OTOD 1KSKA 2K6PA 1KSVA 2KTLA 4OUDA 4LFAD 1I94D 1XNRD 1N33D 3KBGA 4DV3D 4DR7D 4DUZD 4DV7D 4AQYD 4DUYD 2ISTA 2UU9D 4NXMD 4JI2D 4OX9D 4DR5D 4YY3D 4JI4D 4LF9D 2UUCD 4JI7D 4GKKD 4DR4D 1J5ED 4X62D 4JI5D 1H3EA 4DR6D 1KSLA 2VQFD 4DV1D 4LFCD 1HNWD 2UUBD 4X64D 2ZM6D 1N32D 4B3MD 2HHHD 1DM9A 4B3TD 1IBMD 4DV6D 2UXCD 1XMQD 1HNXD 4LGTA 2UUAD 5IWAD 1N36D 4NXND 4YHHD 4DR3D 1C05A 1HNZD 4JYAD 3HP7A 4LF5D 4JI3D 2F4VD 1XNQD 4DV2D 4JI6D 4LF4D 1HR0D 4DR2D 4K0KD 1XMOD 4B3RD 4DV0D 4B3SD 4JI8D 4KHPD 1FJGD 4LF7D 4JI0D 4DR1D 1N34D 4LF8D 4LFBD 1FKAD 4JI1D 2JANA 4X65D 1IBLD 3T1HD 1IBKD 2UXDD 4JV5D 4DV4D 1VIOA 4GKJD 1P9KA 4DV5D 4LF6D 3T1YD 1C06A 2E5LD
chains in the Genus database with same CATH superfamily
5BR8D 2VQED 4X66D 3DH3A 1JH3A 1H3FA 5LMUD 2UXBD 5LMND 3OTOD 1KSKA 1Y8XB 2K6PA 1KSVA 2KTLA 4OUDA 3ONGA 4LFAD 1I94D 1XNRD 1N33D 5FLXE 3KBGA 4DV3D 4DR7D 4DUZD 4DV7D 4AQYD 4II2A 4DUYD 2ISTA 3KYDB 2UU9D 4NXMD 4NNJA 4JI2D 4OX9D 4W5VB 4DR5D 4YY3D 2NVUB 4JI4D 3JAME 4LF9D 4II3A 2UUCD 4JI7D 4GKKD 4DR4D 1J5ED 4X62D 4JI5D 1H3EA 4DR6D 1KSLA 5KNLA 2VQFD 4DV1D 4LFCD 3KYCB 1HNWD 2UUBD 4X64D 2ZM6D 5A2QE 3J81E 1N32D 4B3MD 5FQ2B 2HHHD 1DM9A 4B3TD 1IBMD 4DV6D 3J7AF 2UXCD 1XMQD 1HNXD 1Y8RB 3ONHA 4LGTA 2UUAD 5LL6S 5IWAD 1N36D 2LQ7A 2ZTBA 4NXND 4YHHD 4DR3D 1C05A 1HNZD 4JYAD 3HP7A 4LF5D 4JI3D 2F4VD 1XNQD 4DV2D 4JI6D 4LF4D 2I1SA 1HR0D 4DR2D 4K0KD 1XMOD 4B3RD 4DV0D 4B3SD 3J80E 5IT9E 4JI8D 4KHPD 1FJGD 4LF7D 4JI0D 4DR1D 1N34D 4LF8D 4LFBD 3FN1A 1FKAD 4JI1D 2JANA 4X65D 1IBLD 3T1HD 1Y8QB 1IBKD 2UXDD 4JV5D 4DV4D 1VIOA 4GKJD 2L3NA 1P9KA 4DV5D 4LF6D 3T1YD 3CMMA 1C06A 2E5LD
chains in the Genus database with same CATH topology
5BR8D 2VQED 4X66D 3DH3A 1JH3A 1H3FA 5LMUD 2UXBD 5LMND 3OTOD 1KSKA 2K6PA 1KSVA 2KTLA 4OUDA 4LFAD 1I94D 1XNRD 1N33D 3KBGA 4DV3D 4DR7D 4DUZD 4DV7D 4AQYD 4DUYD 2ISTA 2UU9D 4NXMD 4JI2D 4OX9D 4DR5D 4YY3D 4JI4D 4LF9D 2UUCD 4JI7D 4GKKD 4DR4D 1J5ED 4X62D 4JI5D 1H3EA 4DR6D 1KSLA 2VQFD 4DV1D 4LFCD 1HNWD 2UUBD 4X64D 2ZM6D 1N32D 4B3MD 2HHHD 1DM9A 4B3TD 1IBMD 4DV6D 2UXCD 1XMQD 1HNXD 4LGTA 2UUAD 5IWAD 1N36D 4NXND 4YHHD 4DR3D 1C05A 1HNZD 4JYAD 3HP7A 4LF5D 4JI3D 2F4VD 1XNQD 4DV2D 4JI6D 4LF4D 1HR0D 4DR2D 4K0KD 1XMOD 4B3RD 4DV0D 4B3SD 4JI8D 4KHPD 1FJGD 4LF7D 4JI0D 4DR1D 1N34D 4LF8D 4LFBD 1FKAD 4JI1D 2JANA 4X65D 1IBLD 3T1HD 1IBKD 2UXDD 4JV5D 4DV4D 1VIOA 4GKJD 2L3NA 1P9KA 4DV5D 4LF6D 3T1YD 1C06A 2E5LD
chains in the Genus database with same CATH homology


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