2VQFN

Modified uridines with c5-methylene substituents at the first position of the trna anticodon stabilize u-g wobble pairing during decoding
Total Genus 8
Loading diagram...

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
8
sequence length
60
structure length
60
Chain Sequence
ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
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
molecule keywords 16S RRNA
total genus 8
structure length 60
sequence length 60
ec nomenclature
pdb deposition date 2008-03-14

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
N PF00253 Ribosomal_S14 Ribosomal protein S14p/S29e
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
4.10.830.10 Few Secondary Structures Irregular 30s Ribosomal Protein S14; Chain N 30s Ribosomal Protein S14; Chain N 2vqfN00
3JAMd 4GKJN 4LF4N 2VQFN 4DUZN 4DV2N 1HR0N 1IBMN 5A2Qd 5BR8N 1N34N 4JI7N 3T1YN 4GKKN 4JI4N 2UUAN 1IBLN 4JI1N 4DV4N 4JI3N 1XMQN 4LF5N 4LF9N 2UXCN 4JYAN 4YHHN 4LF8N 3J80d 4DV6N 4YY3N 1XNQN 1IBKN 4DR7N 2UXBN 1J5EN 4DV0N 2UUCN 5LMUN 2VQEN 4X64N 4DR2N 5IT9d 1N33N 2HHHN 5IWAN 5FLXd 1HNXN 3OTON 4X66N 4B3RN 4X62N 4OX9N 4NXMN 4LFBN 1I94N 4B3TN 4DV7N 4DV5N 1HNWN 3T1HN 1XMON 4K0KN 1N32N 4JI8N 4JI0N 1FJGN 1XNRN 1HNZN 4DR3N 4LFCN 4DUYN 4LF7N 2UUBN 4KHPN 2UU9N 4NXNN 4DR4N 4JV5N 4DR1N 4JI2N 4B3SN 4DV3N 3J7AT 3J81d 4X65N 4DV1N 4LFAN 1N36N 2F4VN 4JI5N 4LF6N 2ZM6N 4DR6N 2UXDN 5LMNN 4JI6N 4B3MN 2E5LN 4AQYN 4DR5N
chains in the Genus database with same CATH superfamily
3JAMd 4GKJN 4LF4N 2VQFN 4DUZN 4DV2N 1HR0N 1IBMN 5A2Qd 5BR8N 1N34N 4JI7N 3T1YN 4GKKN 4JI4N 2UUAN 1IBLN 4JI1N 4DV4N 4JI3N 1XMQN 4LF5N 4LF9N 2UXCN 4JYAN 4YHHN 4LF8N 3J80d 4DV6N 4YY3N 1XNQN 1IBKN 4DR7N 2UXBN 1J5EN 4DV0N 2UUCN 5LMUN 2VQEN 4X64N 4DR2N 5IT9d 1N33N 2HHHN 5IWAN 5FLXd 1HNXN 3OTON 4X66N 4B3RN 4X62N 4OX9N 4NXMN 4LFBN 1I94N 4B3TN 4DV7N 4DV5N 1HNWN 3T1HN 1XMON 4K0KN 1N32N 4JI8N 4JI0N 1FJGN 1XNRN 1HNZN 4DR3N 4LFCN 4DUYN 4LF7N 2UUBN 4KHPN 2UU9N 4NXNN 4DR4N 4JV5N 4DR1N 4JI2N 4B3SN 4DV3N 3J7AT 3J81d 4X65N 4DV1N 4LFAN 1N36N 2F4VN 4JI5N 4LF6N 2ZM6N 4DR6N 2UXDN 5LMNN 4JI6N 4B3MN 2E5LN 4AQYN 4DR5N
chains in the Genus database with same CATH topology
3JAMd 4GKJN 4LF4N 2VQFN 4DUZN 4DV2N 1HR0N 1IBMN 5A2Qd 5BR8N 1N34N 4JI7N 3T1YN 4GKKN 4JI4N 2UUAN 1IBLN 4JI1N 4DV4N 4JI3N 1XMQN 4LF5N 4LF9N 2UXCN 4JYAN 4YHHN 4LF8N 3J80d 4DV6N 4YY3N 1XNQN 1IBKN 4DR7N 2UXBN 1J5EN 4DV0N 2UUCN 5LMUN 2VQEN 4X64N 4DR2N 5IT9d 1N33N 2HHHN 5IWAN 5FLXd 1HNXN 3OTON 4X66N 4B3RN 4X62N 4OX9N 4NXMN 4LFBN 1I94N 4B3TN 4DV7N 4DV5N 1HNWN 3T1HN 1XMON 4K0KN 1N32N 4JI8N 4JI0N 1FJGN 1XNRN 1HNZN 4DR3N 4LFCN 4DUYN 4LF7N 2UUBN 4KHPN 2UU9N 4NXNN 4DR4N 4JV5N 4DR1N 4JI2N 4B3SN 4DV3N 3J7AT 3J81d 4X65N 4DV1N 4LFAN 1N36N 2F4VN 4JI5N 4LF6N 2ZM6N 4DR6N 2UXDN 5LMNN 4JI6N 4B3MN 2E5LN 4AQYN 4DR5N
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3JAM d;  4GKJ N;  4LF4 N;  2VQF N;  4DUZ N;  4DV2 N;  1HR0 N;  1IBM N;  5A2Q d;  5BR8 N;  1N34 N;  4JI7 N;  3T1Y N;  4GKK N;  4JI4 N;  2UUA N;  1IBL N;  4JI1 N;  4DV4 N;  4JI3 N;  1XMQ N;  4LF5 N;  4LF9 N;  2UXC N;  4JYA N;  4YHH N;  4LF8 N;  3J80 d;  4DV6 N;  4YY3 N;  1XNQ N;  1IBK N;  4DR7 N;  2UXB N;  1J5E N;  4DV0 N;  2UUC N;  5LMU N;  2VQE N;  4X64 N;  4DR2 N;  5IT9 d;  1N33 N;  2HHH N;  5IWA N;  5FLX d;  1HNX N;  3OTO N;  4X66 N;  4B3R N;  4X62 N;  4OX9 N;  4NXM N;  4LFB N;  1I94 N;  4B3T N;  4DV7 N;  4DV5 N;  1HNW N;  3T1H N;  1XMO N;  4K0K N;  1N32 N;  4JI8 N;  4JI0 N;  1FJG N;  1XNR N;  1HNZ N;  4DR3 N;  4LFC N;  4DUY N;  4LF7 N;  2UUB N;  4KHP N;  2UU9 N;  4NXN N;  4DR4 N;  4JV5 N;  4DR1 N;  4JI2 N;  4B3S N;  4DV3 N;  3J7A T;  3J81 d;  4X65 N;  4DV1 N;  4LFA N;  1N36 N;  2F4V N;  4JI5 N;  4LF6 N;  2ZM6 N;  4DR6 N;  2UXD N;  5LMN N;  4JI6 N;  4B3M N;  2E5L N;  4AQY N;  4DR5 N; 
#chains in the Genus database with same CATH topology
 3JAM d;  4GKJ N;  4LF4 N;  2VQF N;  4DUZ N;  4DV2 N;  1HR0 N;  1IBM N;  5A2Q d;  5BR8 N;  1N34 N;  4JI7 N;  3T1Y N;  4GKK N;  4JI4 N;  2UUA N;  1IBL N;  4JI1 N;  4DV4 N;  4JI3 N;  1XMQ N;  4LF5 N;  4LF9 N;  2UXC N;  4JYA N;  4YHH N;  4LF8 N;  3J80 d;  4DV6 N;  4YY3 N;  1XNQ N;  1IBK N;  4DR7 N;  2UXB N;  1J5E N;  4DV0 N;  2UUC N;  5LMU N;  2VQE N;  4X64 N;  4DR2 N;  5IT9 d;  1N33 N;  2HHH N;  5IWA N;  5FLX d;  1HNX N;  3OTO N;  4X66 N;  4B3R N;  4X62 N;  4OX9 N;  4NXM N;  4LFB N;  1I94 N;  4B3T N;  4DV7 N;  4DV5 N;  1HNW N;  3T1H N;  1XMO N;  4K0K N;  1N32 N;  4JI8 N;  4JI0 N;  1FJG N;  1XNR N;  1HNZ N;  4DR3 N;  4LFC N;  4DUY N;  4LF7 N;  2UUB N;  4KHP N;  2UU9 N;  4NXN N;  4DR4 N;  4JV5 N;  4DR1 N;  4JI2 N;  4B3S N;  4DV3 N;  3J7A T;  3J81 d;  4X65 N;  4DV1 N;  4LFA N;  1N36 N;  2F4V N;  4JI5 N;  4LF6 N;  2ZM6 N;  4DR6 N;  2UXD N;  5LMN N;  4JI6 N;  4B3M N;  2E5L N;  4AQY N;  4DR5 N; 
#chains in the Genus database with same CATH homology
 3JAM d;  4GKJ N;  4LF4 N;  2VQF N;  4DUZ N;  4DV2 N;  1HR0 N;  1IBM N;  5A2Q d;  5BR8 N;  1N34 N;  4JI7 N;  3T1Y N;  4GKK N;  4JI4 N;  2UUA N;  1IBL N;  4JI1 N;  4DV4 N;  4JI3 N;  1XMQ N;  4LF5 N;  4LF9 N;  2UXC N;  4JYA N;  4YHH N;  4LF8 N;  3J80 d;  4DV6 N;  4YY3 N;  1XNQ N;  1IBK N;  4DR7 N;  2UXB N;  1J5E N;  4DV0 N;  2UUC N;  5LMU N;  2VQE N;  4X64 N;  4DR2 N;  5IT9 d;  1N33 N;  2HHH N;  5IWA N;  5FLX d;  1HNX N;  3OTO N;  4X66 N;  4B3R N;  4X62 N;  4OX9 N;  4NXM N;  4LFB N;  1I94 N;  4B3T N;  4DV7 N;  4DV5 N;  1HNW N;  3T1H N;  1XMO N;  4K0K N;  1N32 N;  4JI8 N;  4JI0 N;  1FJG N;  1XNR N;  1HNZ N;  4DR3 N;  4LFC N;  4DUY N;  4LF7 N;  2UUB N;  4KHP N;  2UU9 N;  4NXN N;  4DR4 N;  4JV5 N;  4DR1 N;  4JI2 N;  4B3S N;  4DV3 N;  3J7A T;  3J81 d;  4X65 N;  4DV1 N;  4LFA N;  1N36 N;  2F4V N;  4JI5 N;  4LF6 N;  2ZM6 N;  4DR6 N;  2UXD N;  5LMN N;  4JI6 N;  4B3M N;  2E5L N;  4AQY N;  4DR5 N; 
...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...