2DSD
Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and AMP
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 | 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 | 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 | 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 | 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 A 301 |
| Chain | Residue |
| A | GLN82 |
| A | ARG84 |
| A | ALA96 |
| A | GLU116 |
| A | AMP401 |
| A | HOH417 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 302 |
| Chain | Residue |
| A | GLU166 |
| A | AMP401 |
| A | GLU112 |
| A | GLU115 |
| A | GLU116 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 303 |
| Chain | Residue |
| A | LEU98 |
| A | GLU112 |
| A | AMP401 |
| A | HOH431 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 304 |
| Chain | Residue |
| B | ALA96 |
| B | GLU116 |
| B | GLU166 |
| B | AMP402 |
| B | HOH419 |
| B | HOH440 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG B 305 |
| Chain | Residue |
| B | GLU112 |
| B | GLU116 |
| B | GLU166 |
| B | AMP402 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG B 306 |
| Chain | Residue |
| B | GLU112 |
| B | AMP402 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE AMP A 401 |
| Chain | Residue |
| A | TRP28 |
| A | ALA96 |
| A | GLY97 |
| A | GLU112 |
| A | GLU116 |
| A | GLU166 |
| A | MG301 |
| A | MG302 |
| A | MG303 |
| A | HOH417 |
| B | TRP46 |
| B | GLU47 |
| site_id | AC8 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE AMP B 402 |
| Chain | Residue |
| A | THR45 |
| A | TRP46 |
| A | GLU47 |
| B | VAL29 |
| B | ARG51 |
| B | ALA96 |
| B | GLY97 |
| B | LEU98 |
| B | GLU112 |
| B | GLU116 |
| B | GLU166 |
| B | MG304 |
| B | MG305 |
| B | MG306 |
| B | HOH419 |
| B | HOH442 |
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 | 280 |
| Details | Domain: {"description":"Nudix hydrolase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00794","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 42 |
| Details | Motif: {"description":"Nudix box"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18462755","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21768126","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18462755","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21768126","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"17052728","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"27257257","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1mqw |
| Chain | Residue | Details |
| A | ASP164 | |
| A | ARG84 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1mqw |
| Chain | Residue | Details |
| B | ASP164 | |
| B | ARG84 |
