6VCK
Crystal structure of E.coli RppH-DapF in complex with GDP, Mg2+ and F-
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 | 5 |
| Details | binding site for residue MG B 201 |
| Chain | Residue |
| B | GLU53 |
| B | GDP204 |
| B | F206 |
| B | HOH313 |
| B | HOH353 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 202 |
| Chain | Residue |
| B | GDP204 |
| B | F206 |
| B | GLU53 |
| B | GLU57 |
| B | GLU120 |
| B | MG203 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 203 |
| Chain | Residue |
| B | GLN37 |
| B | GLU57 |
| B | GLU120 |
| B | MG202 |
| B | GDP204 |
| site_id | AC4 |
| Number of Residues | 17 |
| Details | binding site for residue GDP B 204 |
| Chain | Residue |
| B | ASN10 |
| B | ARG27 |
| B | GLN37 |
| B | GLY38 |
| B | GLY39 |
| B | GLU53 |
| B | GLU57 |
| B | TYR77 |
| B | GLN95 |
| B | GLU120 |
| B | LYS140 |
| B | MG201 |
| B | MG202 |
| B | MG203 |
| B | F206 |
| B | HOH303 |
| B | HOH313 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | binding site for residue CL B 205 |
| Chain | Residue |
| B | ARG62 |
| B | ARG62 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue F B 206 |
| Chain | Residue |
| B | GLU53 |
| B | MG201 |
| B | MG202 |
| B | GDP204 |
| B | HOH353 |
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 |
