6D1V
Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0008047 | molecular_function | enzyme activator activity |
| A | 0008652 | biological_process | amino acid biosynthetic process |
| A | 0008837 | molecular_function | diaminopimelate epimerase activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0009089 | biological_process | lysine biosynthetic process via diaminopimelate |
| A | 0016853 | molecular_function | isomerase activity |
| A | 0042803 | molecular_function | protein homodimerization activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006402 | biological_process | mRNA catabolic process |
| B | 0008033 | biological_process | tRNA processing |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0016818 | molecular_function | hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides |
| B | 0034353 | molecular_function | mRNA 5'-diphosphatase activity |
| B | 0050779 | biological_process | RNA destabilization |
| B | 0110153 | molecular_function | RNA NAD-cap (NMN-forming) hydrolase activity |
| B | 0110154 | biological_process | RNA decapping |
| B | 0110155 | biological_process | NAD-cap decapping |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue GOL A 801 |
| Chain | Residue |
| A | LEU38 |
| A | TYR52 |
| A | HIS59 |
| A | THR99 |
| A | HOH903 |
| A | HOH907 |
| A | HOH938 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 802 |
| Chain | Residue |
| A | HOH922 |
| A | HOH953 |
| B | PRO80 |
| B | ARG82 |
| A | GLN44 |
| A | ASN64 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 803 |
| Chain | Residue |
| A | ARG103 |
| A | MET104 |
| A | VAL105 |
| A | ASN117 |
| A | HOH932 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 804 |
| Chain | Residue |
| A | HIS266 |
| B | GLN114 |
| B | ASP122 |
| B | HOH350 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue CL A 805 |
| Chain | Residue |
| A | GLY76 |
| A | ARG78 |
| A | CYS79 |
| A | HOH982 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue CL A 806 |
| Chain | Residue |
| A | MET141 |
| A | ARG142 |
| A | ARG184 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue CL A 807 |
| Chain | Residue |
| A | ASN157 |
| A | ARG209 |
| B | LYS81 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue MG B 201 |
| Chain | Residue |
| B | GLU53 |
| B | MG202 |
| B | HOH314 |
| B | HOH327 |
| B | HOH369 |
| C | APC1 |
| C | HOH102 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue MG B 202 |
| Chain | Residue |
| B | GLU53 |
| B | GLU56 |
| B | GLU57 |
| B | GLU120 |
| B | MG201 |
| B | MG203 |
| B | HOH369 |
| C | APC1 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 203 |
| Chain | Residue |
| B | GLN37 |
| B | GLU57 |
| B | GLU120 |
| B | MG202 |
| B | HOH344 |
| C | APC1 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue GOL B 204 |
| Chain | Residue |
| B | ALA46 |
| B | GLU47 |
| B | PHE100 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 205 |
| Chain | Residue |
| A | ASN22 |
| B | ASP142 |
| B | ARG145 |
| B | HOH312 |
| B | HOH352 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 206 |
| Chain | Residue |
| B | ILE111 |
| B | ASN112 |
| B | MET113 |
| B | GLN114 |
| B | TRP124 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue CL B 207 |
| Chain | Residue |
| B | SER61 |
| B | SER61 |
| B | ARG62 |
| B | ARG62 |
| B | HOH427 |
| B | HOH427 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"HAMAP-Rule","id":"MF_00197","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00197","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00197","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Site: {"description":"Could be important to modulate the pK values of the two catalytic cysteine residues","evidences":[{"source":"HAMAP-Rule","id":"MF_00197","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | Site: {"description":"Important for dimerization","evidences":[{"source":"PubMed","id":"23426375","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 143 |
| Details | Domain: {"description":"Nudix hydrolase"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 21 |
| Details | Motif: {"description":"Nudix box"} |
| Chain | Residue | Details |
