2DSC
Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0003723 | molecular_function | RNA binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005829 | cellular_component | cytosol |
| A | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| A | 0006338 | biological_process | chromatin remodeling |
| A | 0006753 | biological_process | nucleoside phosphate metabolic process |
| A | 0009117 | biological_process | nucleotide metabolic process |
| A | 0009191 | biological_process | ribonucleoside diphosphate catabolic process |
| A | 0016462 | molecular_function | pyrophosphatase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| A | 0019144 | molecular_function | ADP-sugar diphosphatase activity |
| A | 0019303 | biological_process | D-ribose catabolic process |
| A | 0019693 | biological_process | ribose phosphate metabolic process |
| A | 0030515 | molecular_function | snoRNA binding |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0044715 | molecular_function | 8-oxo-dGDP phosphatase activity |
| A | 0044716 | molecular_function | 8-oxo-GDP phosphatase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047631 | molecular_function | ADP-ribose diphosphatase activity |
| A | 0055086 | biological_process | nucleobase-containing small molecule metabolic process |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0140933 | molecular_function | 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity |
| A | 1990966 | biological_process | ATP generation from poly-ADP-D-ribose |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005829 | cellular_component | cytosol |
| B | 0006139 | biological_process | nucleobase-containing compound metabolic process |
| B | 0006338 | biological_process | chromatin remodeling |
| B | 0006753 | biological_process | nucleoside phosphate metabolic process |
| B | 0009117 | biological_process | nucleotide metabolic process |
| B | 0009191 | biological_process | ribonucleoside diphosphate catabolic process |
| B | 0016462 | molecular_function | pyrophosphatase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0016779 | molecular_function | nucleotidyltransferase activity |
| B | 0016787 | molecular_function | hydrolase activity |
| B | 0017110 | molecular_function | nucleoside diphosphate phosphatase activity |
| B | 0019144 | molecular_function | ADP-sugar diphosphatase activity |
| B | 0019303 | biological_process | D-ribose catabolic process |
| B | 0019693 | biological_process | ribose phosphate metabolic process |
| B | 0030515 | molecular_function | snoRNA binding |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0044715 | molecular_function | 8-oxo-dGDP phosphatase activity |
| B | 0044716 | molecular_function | 8-oxo-GDP phosphatase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047631 | molecular_function | ADP-ribose diphosphatase activity |
| B | 0055086 | biological_process | nucleobase-containing small molecule metabolic process |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0140933 | molecular_function | 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity |
| B | 1990966 | biological_process | ATP generation from poly-ADP-D-ribose |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 301 |
| Chain | Residue |
| A | APR402 |
| B | ALA96 |
| B | GLU112 |
| B | GLU116 |
| B | HOH418 |
| B | HOH448 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 302 |
| Chain | Residue |
| A | HOH409 |
| A | HOH433 |
| B | APR401 |
| A | ALA96 |
| A | GLU116 |
| A | GLU166 |
| site_id | AC3 |
| Number of Residues | 26 |
| Details | BINDING SITE FOR RESIDUE APR B 401 |
| Chain | Residue |
| A | TRP28 |
| A | VAL29 |
| A | ARG51 |
| A | ARG84 |
| A | ALA96 |
| A | GLY97 |
| A | LEU98 |
| A | MET132 |
| A | GLU166 |
| A | ARG196 |
| A | MG302 |
| A | HOH451 |
| A | HOH486 |
| A | HOH487 |
| B | TRP46 |
| B | GLU47 |
| B | ASP133 |
| B | GLY135 |
| B | LEU136 |
| B | HOH472 |
| B | HOH476 |
| B | HOH480 |
| B | HOH484 |
| B | HOH485 |
| B | HOH507 |
| B | HOH529 |
| site_id | AC4 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE APR A 402 |
| Chain | Residue |
| A | TRP46 |
| A | GLU47 |
| A | ASP133 |
| A | GLY135 |
| A | LEU136 |
| A | HOH444 |
| A | HOH461 |
| B | TRP28 |
| B | VAL29 |
| B | ARG51 |
| B | ARG84 |
| B | ALA96 |
| B | GLY97 |
| B | LEU98 |
| B | GLU166 |
| B | MG301 |
| B | HOH486 |
| B | HOH504 |
| B | HOH517 |
| B | HOH547 |
Functional Information from PROSITE/UniProt
| site_id | PS00893 |
| Number of Residues | 22 |
| Details | NUDIX_BOX Nudix box signature. GliddgEtpeaAAlRELeEEtG |
| Chain | Residue | Details |
| A | GLY97-GLY118 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:17052728, ECO:0000269|PubMed:18462755, ECO:0000269|PubMed:21768126 |
| Chain | Residue | Details |
| B | TRP28 | |
| B | ARG84 | |
| A | TRP28 | |
| A | ARG84 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17052728, ECO:0000269|PubMed:18462755, ECO:0000269|PubMed:21768126 |
| Chain | Residue | Details |
| B | TRP46 | |
| B | ARG51 | |
| B | ALA96 | |
| B | GLU112 | |
| B | GLU116 | |
| B | GLU166 | |
| A | TRP46 | |
| A | ARG51 | |
| A | ALA96 | |
| A | GLU112 | |
| A | GLU116 | |
| A | GLU166 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:17052728 |
| Chain | Residue | Details |
| A | LEU98 | |
| A | ASP133 | |
| B | LEU98 | |
| B | ASP133 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:22223895 |
| Chain | Residue | Details |
| A | MET1 | |
| B | MET1 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER3 | |
| B | SER3 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| A | SER10 | |
| B | SER10 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:27257257 |
| Chain | Residue | Details |
| A | THR45 | |
| B | THR45 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455 |
| Chain | Residue | Details |
| A | TYR74 | |
| B | TYR74 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS210 | |
| B | LYS210 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS42 | |
| A | LYS42 |
