1N33D

Structure of the thermus thermophilus 30s ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin
Total Genus 57
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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
57
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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publication title Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
pubmed doi rcsb
molecule tags Ribosome
molecule keywords 16S RIBOSOMAL RNA
total genus 57
structure length 208
sequence length 208
ec nomenclature
pdb deposition date 2002-10-25

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 1n33D01
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 1n33D02
4JI0D 4NXMD 4X64D 4LFBD 4B3MD 2HHHD 1XMOD 1J5ED 1P9KA 4X65D 4B3TD 1KSVA 2ISTA 3OTOD 2UXDD 3T1HD 1FJGD 2VQFD 4JI2D 2UUAD 1H3FA 3T1YD 1HR0D 2UU9D 4NXND 4DV2D 4GKJD 1C06A 1JH3A 4LFCD 1N32D 4DR3D 2K6PA 4X62D 3KBGA 5BR8D 2ZM6D 4LF9D 4JI5D 5IWAD 1XMQD 4DV5D 4JV5D 4OUDA 2UXBD 5LMND 1N36D 4JI3D 4YY3D 4LGTA 4B3RD 4DR5D 4AQYD 4DR7D 4DR2D 1HNZD 4JI1D 4X66D 1IBLD 4B3SD 2VQED 2JANA 4LF8D 4JI7D 3DH3A 4JYAD 4DR1D 1KSLA 1IBKD 4LF6D 1HNWD 4GKKD 4K0KD 1VIOA 4JI8D 1I94D 4DV3D 2E5LD 1KSKA 2F4VD 4LF5D 4DV4D 2UUBD 4YHHD 4KHPD 1DM9A 3HP7A 4DUYD 1IBMD 1XNRD 1FKAD 4DR6D 4JI6D 4DV1D 5LMUD 1H3EA 4LF4D 4OX9D 4LFAD 4DR4D 2UUCD 2UXCD 4DV7D 1C05A 4DV0D 1N33D 4DV6D 4DUZD 4LF7D 2KTLA 1N34D 1XNQD 1HNXD 4JI4D
chains in the Genus database with same CATH superfamily
4JI0D 4NXMD 1Y8QB 5FQ2B 4X64D 4LFBD 4B3MD 2HHHD 1XMOD 1J5ED 1P9KA 4X65D 5KNLA 4B3TD 1KSVA 2ISTA 3OTOD 2UXDD 3T1HD 2ZTBA 5A2QE 1FJGD 3J7AF 2VQFD 4JI2D 2UUAD 4II3A 1H3FA 2I1SA 3ONHA 3T1YD 1HR0D 2UU9D 4NXND 4DV2D 4GKJD 1C06A 1JH3A 4LFCD 1N32D 4DR3D 2K6PA 4X62D 3KBGA 5BR8D 2ZM6D 3KYDB 4LF9D 4JI5D 5IWAD 1XMQD 4DV5D 5FLXE 3JAME 4JV5D 4OUDA 2UXBD 5LMND 1N36D 3ONGA 4JI3D 4YY3D 4LGTA 4B3RD 4DR5D 4AQYD 4DR7D 4DR2D 1Y8XB 1HNZD 4JI1D 4X66D 1IBLD 4B3SD 2VQED 4NNJA 2JANA 4LF8D 4JI7D 3DH3A 4JYAD 4DR1D 1KSLA 1IBKD 4LF6D 1HNWD 4GKKD 4K0KD 1VIOA 4JI8D 1I94D 4DV3D 2E5LD 1KSKA 4W5VB 2F4VD 4LF5D 3FN1A 4DV4D 2UUBD 2NVUB 4YHHD 4KHPD 2L3NA 1DM9A 1Y8RB 3HP7A 4DUYD 1IBMD 1XNRD 1FKAD 4DR6D 4JI6D 4DV1D 5LMUD 3J81E 1H3EA 4LF4D 4OX9D 2LQ7A 4LFAD 4DR4D 5LL6S 2UUCD 3KYCB 2UXCD 4DV7D 1C05A 4II2A 4DV0D 1N33D 3J80E 4DV6D 4DUZD 5IT9E 4LF7D 2KTLA 1N34D 1XNQD 3CMMA 1HNXD 4JI4D
chains in the Genus database with same CATH topology
4JI0D 4NXMD 4X64D 4LFBD 4B3MD 2HHHD 1XMOD 1J5ED 1P9KA 4X65D 4B3TD 1KSVA 2ISTA 3OTOD 2UXDD 3T1HD 1FJGD 2VQFD 4JI2D 2UUAD 1H3FA 3T1YD 1HR0D 2UU9D 4NXND 4DV2D 4GKJD 1C06A 1JH3A 4LFCD 1N32D 4DR3D 2K6PA 4X62D 3KBGA 5BR8D 2ZM6D 4LF9D 4JI5D 5IWAD 1XMQD 4DV5D 4JV5D 4OUDA 2UXBD 5LMND 1N36D 4JI3D 4YY3D 4LGTA 4B3RD 4DR5D 4AQYD 4DR7D 4DR2D 1HNZD 4JI1D 4X66D 1IBLD 4B3SD 2VQED 2JANA 4LF8D 4JI7D 3DH3A 4JYAD 4DR1D 1KSLA 1IBKD 4LF6D 1HNWD 4GKKD 4K0KD 1VIOA 4JI8D 1I94D 4DV3D 2E5LD 1KSKA 2F4VD 4LF5D 4DV4D 2UUBD 4YHHD 4KHPD 2L3NA 1DM9A 3HP7A 4DUYD 1IBMD 1XNRD 1FKAD 4DR6D 4JI6D 4DV1D 5LMUD 1H3EA 4LF4D 4OX9D 4LFAD 4DR4D 2UUCD 2UXCD 4DV7D 1C05A 4DV0D 1N33D 4DV6D 4DUZD 4LF7D 2KTLA 1N34D 1XNQD 1HNXD 4JI4D
chains in the Genus database with same CATH homology


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