5LMUD

Structure of bacterial 30s-if3-mrna-trna translation pre-initiation complex, closed form (state-4)
Total Genus 51
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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
51
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 Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.
pubmed doi rcsb
source organism Thermus thermophilus hb8
molecule tags Ribosome
total genus 51
structure length 208
sequence length 208
ec nomenclature
pdb deposition date 2016-08-01

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 5lmuD01
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 5lmuD02
2VQED 1N36D 1C05A 4B3RD 2VQFD 4DV6D 4DUYD 4DV1D 4DR1D 4LF9D 4LFAD 1J5ED 1FJGD 4DR6D 1HNWD 1XMQD 1IBMD 4LF6D 4LFBD 1HNXD 1H3FA 4JI7D 1KSLA 4NXMD 4JI6D 1IBLD 1XNQD 1FKAD 4JI0D 4LGTA 4JI8D 4AQYD 4X64D 5LMUD 4JV5D 4DR2D 2E5LD 4K0KD 4OUDA 1JH3A 5BR8D 2KTLA 4DR3D 4B3MD 4LF4D 3OTOD 4DUZD 2F4VD 1P9KA 2HHHD 4YHHD 4JI5D 4X66D 4JI2D 4LF8D 2UUCD 1N34D 1C06A 4DV7D 2UXCD 1XMOD 2UXDD 2ISTA 1N32D 1N33D 4JI3D 4B3SD 4DR7D 3DH3A 4LFCD 4KHPD 2K6PA 4JYAD 4JI4D 4OX9D 4GKJD 4DV3D 2UU9D 3HP7A 3T1HD 4NXND 1KSVA 1H3EA 1KSKA 2JANA 2UUBD 4LF5D 4JI1D 4DR4D 4B3TD 3KBGA 1VIOA 4DV2D 5IWAD 4DV5D 4X62D 4X65D 4DR5D 2UXBD 1IBKD 5LMND 1XNRD 2ZM6D 1HNZD 3T1YD 4LF7D 1I94D 1HR0D 2UUAD 4DV4D 4DV0D 4GKKD 4YY3D 1DM9A
chains in the Genus database with same CATH superfamily
2VQED 5FLXE 1N36D 1C05A 4B3RD 2VQFD 4DV6D 4DUYD 4DV1D 4DR1D 4LF9D 3CMMA 4LFAD 3FN1A 1J5ED 1FJGD 3ONGA 4DR6D 1HNWD 1XMQD 1IBMD 4LF6D 5FQ2B 4LFBD 1HNXD 1H3FA 4JI7D 1KSLA 4NXMD 4JI6D 1IBLD 1XNQD 1FKAD 4JI0D 4LGTA 4JI8D 4AQYD 4X64D 1Y8XB 5LMUD 4JV5D 4DR2D 5LL6S 1Y8QB 2E5LD 5KNLA 4K0KD 2I1SA 4OUDA 1JH3A 5BR8D 2KTLA 4DR3D 4B3MD 4LF4D 3OTOD 4DUZD 2F4VD 1P9KA 2HHHD 4YHHD 4JI5D 4X66D 3ONHA 4JI2D 3J7AF 4LF8D 2UUCD 1N34D 1C06A 4DV7D 2UXCD 1XMOD 3J80E 4II2A 2UXDD 2ISTA 1N32D 1N33D 4JI3D 4B3SD 4DR7D 3DH3A 4LFCD 4KHPD 2K6PA 4JYAD 4JI4D 4OX9D 4GKJD 4DV3D 2UU9D 3HP7A 3T1HD 4NXND 5A2QE 1KSVA 1H3EA 1KSKA 2JANA 2UUBD 4LF5D 4JI1D 4DR4D 4B3TD 3KBGA 1VIOA 4DV2D 4NNJA 5IWAD 4DV5D 4X62D 4X65D 5IT9E 2NVUB 4DR5D 2ZTBA 2UXBD 3KYDB 1IBKD 5LMND 1XNRD 2ZM6D 3KYCB 1Y8RB 4II3A 1HNZD 3T1YD 4LF7D 1I94D 1HR0D 3JAME 2UUAD 4DV4D 3J81E 4W5VB 2LQ7A 4DV0D 4GKKD 4YY3D 2L3NA 1DM9A
chains in the Genus database with same CATH topology
2VQED 1N36D 1C05A 4B3RD 2VQFD 4DV6D 4DUYD 4DV1D 4DR1D 4LF9D 4LFAD 1J5ED 1FJGD 4DR6D 1HNWD 1XMQD 1IBMD 4LF6D 4LFBD 1HNXD 1H3FA 4JI7D 1KSLA 4NXMD 4JI6D 1IBLD 1XNQD 1FKAD 4JI0D 4LGTA 4JI8D 4AQYD 4X64D 5LMUD 4JV5D 4DR2D 2E5LD 4K0KD 4OUDA 1JH3A 5BR8D 2KTLA 4DR3D 4B3MD 4LF4D 3OTOD 4DUZD 2F4VD 1P9KA 2HHHD 4YHHD 4JI5D 4X66D 4JI2D 4LF8D 2UUCD 1N34D 1C06A 4DV7D 2UXCD 1XMOD 2UXDD 2ISTA 1N32D 1N33D 4JI3D 4B3SD 4DR7D 3DH3A 4LFCD 4KHPD 2K6PA 4JYAD 4JI4D 4OX9D 4GKJD 4DV3D 2UU9D 3HP7A 3T1HD 4NXND 1KSVA 1H3EA 1KSKA 2JANA 2UUBD 4LF5D 4JI1D 4DR4D 4B3TD 3KBGA 1VIOA 4DV2D 5IWAD 4DV5D 4X62D 4X65D 4DR5D 2UXBD 1IBKD 5LMND 1XNRD 2ZM6D 1HNZD 3T1YD 4LF7D 1I94D 1HR0D 2UUAD 4DV4D 4DV0D 4GKKD 4YY3D 2L3NA 1DM9A
chains in the Genus database with same CATH homology


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