6D1QB

Crystal structure of e. coli rpph-dapf complex, monomer
Total Genus 40
204060801001201400510152025303540
Genus TraceResidueGenus

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
40
sequence length
160
structure length
160
Chain Sequence
SMIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMSLQ

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
TI1 (3-6)S7 (94-104)EMPTYS1 (7-16)TII2 (41-44)S2 (22-27)TI2 (17-20)S3 (33-34)TII1 (27-30)S4 (37-39)S6 (75-78)AH1 (46-58)TI3 (61-64)S8 (121-127)TIV2 (112-115)S5 (65-70)3H1 (81-83)TI5 (85-88)3H2 (108-110)TIV3 (114-117)TIV4 (116-119)TIV1 (88-91)AH2 (130-135)3H3 (138-140)AH3 (141-157)Updating...
connected with : NaN
molecule tags Isomerase/hydrolase
source organism Escherichia coli (strain k12)
publication title Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
pubmed doi rcsb
molecule keywords Diaminopimelate epimerase
total genus 40
structure length 160
sequence length 160
ec nomenclature
pdb deposition date 2018-04-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
B PF00293 NUDIX NUDIX domain
Image from the rcsb pdb (www.rcsb.org)
...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...

Application loaded.