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 | 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 | 0016462 | molecular_function | pyrophosphatase activity |
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 | ACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_00197 |
Chain | Residue | Details |
A | CYS73 |
site_id | SWS_FT_FI2 |
Number of Residues | 1 |
Details | ACT_SITE: Proton acceptor => ECO:0000255|HAMAP-Rule:MF_00197 |
Chain | Residue | Details |
A | CYS217 |
site_id | SWS_FT_FI3 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00197 |
Chain | Residue | Details |
A | ASN190 | |
A | GLU208 | |
A | GLY218 | |
A | ASN11 | |
A | GLN44 | |
A | ASN64 | |
A | GLY74 | |
A | ASN157 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | SITE: Could be important to modulate the pK values of the two catalytic cysteine residues => ECO:0000255|HAMAP-Rule:MF_00197 |
Chain | Residue | Details |
A | HIS159 | |
A | GLU208 |
site_id | SWS_FT_FI5 |
Number of Residues | 1 |
Details | SITE: Important for dimerization => ECO:0000269|PubMed:23426375 |
Chain | Residue | Details |
A | ALA268 |