2VQFD

Modified uridines with c5-methylene substituents at the first position of the trna anticodon stabilize u-g wobble pairing during decoding
Total Genus 60
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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
60
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 RRNA
publication title Modified Uridines with C5-Methylene Substituents at the First Position of the tRNA Anticodon Stabilize U.G Wobble Pairing During Decoding.
pubmed doi rcsb
molecule tags Ribosome
total genus 60
structure length 208
sequence length 208
ec nomenclature
pdb deposition date 2008-03-14

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 2vqfD01
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 2vqfD02
4JI5D 4DR2D 1IBLD 4OUDA 2UU9D 1XMQD 1N34D 4K0KD 1VIOA 4DV2D 4DV5D 1KSVA 1N36D 1XNRD 1HNXD 4LFAD 4LFBD 2UXCD 4DV6D 4JI8D 5IWAD 2K6PA 2HHHD 1C05A 1JH3A 1DM9A 4X65D 4DV1D 4DR4D 1FKAD 4AQYD 5LMND 3T1YD 2E5LD 4X62D 4GKKD 4X66D 1I94D 4GKJD 4DR3D 1FJGD 4DV4D 2ISTA 4LF4D 3OTOD 1KSKA 2UXBD 4DV7D 4JV5D 4LF7D 4DR1D 4DUZD 4LFCD 1HNZD 1HR0D 5LMUD 1P9KA 4X64D 4YY3D 2ZM6D 4JI4D 4LF5D 2UUAD 4DR7D 4LF8D 2UUBD 1N33D 1C06A 4LGTA 1IBMD 2VQED 1H3EA 4YHHD 1IBKD 4JI0D 4JI3D 4JI6D 2KTLA 2JANA 4JI2D 1HNWD 2UUCD 2UXDD 4NXMD 4DV3D 4JI7D 1XNQD 4B3RD 4DR5D 1N32D 2F4VD 4OX9D 1J5ED 4NXND 4DV0D 3DH3A 4LF6D 1H3FA 2VQFD 4LF9D 4DUYD 1XMOD 5BR8D 1KSLA 3T1HD 4B3SD 4DR6D 4KHPD 4JI1D 4B3TD 4B3MD 4JYAD 3KBGA 3HP7A
chains in the Genus database with same CATH superfamily
4JI5D 4DR2D 1IBLD 4OUDA 3JAME 2UU9D 1XMQD 3FN1A 1N34D 3ONGA 4K0KD 1VIOA 4DV2D 4DV5D 2ZTBA 4II2A 1Y8RB 1KSVA 1N36D 1XNRD 1HNXD 4LFAD 4LFBD 2UXCD 4DV6D 3J80E 5IT9E 4JI8D 5IWAD 5KNLA 2K6PA 2HHHD 1C05A 1JH3A 1DM9A 4X65D 3J81E 4DV1D 4DR4D 1FKAD 4AQYD 5LMND 5FQ2B 3T1YD 2E5LD 4X62D 4GKKD 4X66D 1I94D 4GKJD 4DR3D 1FJGD 4DV4D 2ISTA 4LF4D 3OTOD 1KSKA 2UXBD 3J7AF 4DV7D 4JV5D 4LF7D 3KYCB 4DR1D 4DUZD 4LFCD 1HNZD 1HR0D 5LMUD 1P9KA 4X64D 4YY3D 2ZM6D 2NVUB 4JI4D 4LF5D 2UUAD 4DR7D 2LQ7A 4LF8D 2UUBD 1N33D 1C06A 4LGTA 5A2QE 1IBMD 2VQED 1H3EA 4YHHD 1IBKD 4JI0D 4JI3D 4JI6D 2KTLA 3ONHA 2JANA 4JI2D 1HNWD 2UUCD 5LL6S 2UXDD 3KYDB 4NXMD 4DV3D 4JI7D 2L3NA 1XNQD 4B3RD 5FLXE 4DR5D 1N32D 2F4VD 4OX9D 1J5ED 4NXND 4DV0D 3DH3A 4LF6D 1Y8QB 1H3FA 2VQFD 4W5VB 4LF9D 4NNJA 1Y8XB 4DUYD 1XMOD 5BR8D 1KSLA 3T1HD 4B3SD 4DR6D 4KHPD 4JI1D 3CMMA 2I1SA 4B3TD 4II3A 4B3MD 4JYAD 3KBGA 3HP7A
chains in the Genus database with same CATH topology
4JI5D 4DR2D 1IBLD 4OUDA 2UU9D 1XMQD 1N34D 4K0KD 1VIOA 4DV2D 4DV5D 1KSVA 1N36D 1XNRD 1HNXD 4LFAD 4LFBD 2UXCD 4DV6D 4JI8D 5IWAD 2K6PA 2HHHD 1C05A 1JH3A 1DM9A 4X65D 4DV1D 4DR4D 1FKAD 4AQYD 5LMND 3T1YD 2E5LD 4X62D 4GKKD 4X66D 1I94D 4GKJD 4DR3D 1FJGD 4DV4D 2ISTA 4LF4D 3OTOD 1KSKA 2UXBD 4DV7D 4JV5D 4LF7D 4DR1D 4DUZD 4LFCD 1HNZD 1HR0D 5LMUD 1P9KA 4X64D 4YY3D 2ZM6D 4JI4D 4LF5D 2UUAD 4DR7D 4LF8D 2UUBD 1N33D 1C06A 4LGTA 1IBMD 2VQED 1H3EA 4YHHD 1IBKD 4JI0D 4JI3D 4JI6D 2KTLA 2JANA 4JI2D 1HNWD 2UUCD 2UXDD 4NXMD 4DV3D 4JI7D 2L3NA 1XNQD 4B3RD 4DR5D 1N32D 2F4VD 4OX9D 1J5ED 4NXND 4DV0D 3DH3A 4LF6D 1H3FA 2VQFD 4LF9D 4DUYD 1XMOD 5BR8D 1KSLA 3T1HD 4B3SD 4DR6D 4KHPD 4JI1D 4B3TD 4B3MD 4JYAD 3KBGA 3HP7A
chains in the Genus database with same CATH homology


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