6DBZ
Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000210 | molecular_function | NAD+ diphosphatase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006974 | biological_process | DNA damage response |
| A | 0008413 | molecular_function | 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0019177 | molecular_function | dihydroneopterin triphosphate pyrophosphohydrolase activity |
| A | 0035529 | molecular_function | NADH pyrophosphatase activity |
| A | 0035539 | molecular_function | 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000210 | molecular_function | NAD+ diphosphatase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006974 | biological_process | DNA damage response |
| B | 0008413 | molecular_function | 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0019177 | molecular_function | dihydroneopterin triphosphate pyrophosphohydrolase activity |
| B | 0035529 | molecular_function | NADH pyrophosphatase activity |
| B | 0035539 | molecular_function | 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 13 |
| Details | binding site for residue IPR A 201 |
| Chain | Residue |
| A | ARG27 |
| A | MG203 |
| A | MG204 |
| A | HOH301 |
| A | HOH377 |
| A | GLY40 |
| A | GLY41 |
| A | HIS42 |
| A | GLU56 |
| A | GLU60 |
| A | TYR87 |
| A | PHE127 |
| A | MG202 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | binding site for residue MG A 202 |
| Chain | Residue |
| A | GLY40 |
| A | GLU56 |
| A | GLU60 |
| A | IPR201 |
| A | MG203 |
| A | MG204 |
| A | HOH301 |
| A | HOH324 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 203 |
| Chain | Residue |
| A | GLY40 |
| A | GLU60 |
| A | IPR201 |
| A | MG202 |
| A | HOH377 |
| A | HOH379 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue MG A 204 |
| Chain | Residue |
| A | GLU56 |
| A | IPR201 |
| A | MG202 |
| A | HOH365 |
| A | HOH380 |
| A | HOH392 |
| A | HOH398 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 205 |
| Chain | Residue |
| A | HOH326 |
| A | HOH330 |
| A | HOH341 |
| A | HOH406 |
| A | HOH409 |
| A | HOH423 |
| site_id | AC6 |
| Number of Residues | 12 |
| Details | binding site for residue IPR B 201 |
| Chain | Residue |
| B | ALA11 |
| B | ARG27 |
| B | GLY40 |
| B | GLY41 |
| B | HIS42 |
| B | GLU60 |
| B | ASN76 |
| B | LYS110 |
| B | MG202 |
| B | MG203 |
| B | MG204 |
| B | HOH340 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 202 |
| Chain | Residue |
| B | GLY40 |
| B | GLU60 |
| B | IPR201 |
| B | HOH304 |
| B | HOH340 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue MG B 203 |
| Chain | Residue |
| B | GLU56 |
| B | IPR201 |
| B | MG204 |
| B | HOH322 |
| B | HOH328 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 204 |
| Chain | Residue |
| B | GLU56 |
| B | GLU60 |
| B | IPR201 |
| B | MG203 |
| B | HOH304 |
| B | HOH317 |
Functional Information from PROSITE/UniProt
| site_id | PS00893 |
| Number of Residues | 22 |
| Details | NUDIX_BOX Nudix box signature. GhlefgEsfeeCAaREVmEEtG |
| Chain | Residue | Details |
| A | GLY41-GLY62 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000250 |
| Chain | Residue | Details |
| A | GLU56 | |
| A | GLU60 | |
| B | GLU56 | |
| B | GLU60 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylserine => ECO:0007744|PubMed:22223895 |
| Chain | Residue | Details |
| A | SER2 | |
| B | SER2 |
