6XDH
Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0016627 | molecular_function | oxidoreductase activity, acting on the CH-CH group of donors |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0016627 | molecular_function | oxidoreductase activity, acting on the CH-CH group of donors |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue ACT A 401 |
| Chain | Residue |
| A | ASP37 |
| A | ASN74 |
| A | GLY77 |
| A | VAL78 |
| A | ASP79 |
| A | HOH509 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | binding site for residue CIT A 402 |
| Chain | Residue |
| A | GLY247 |
| A | GLY248 |
| A | HIS250 |
| A | LYS290 |
| A | THR341 |
| A | TYR343 |
| A | HIS235 |
| A | GLN245 |
| A | LEU246 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue FMT A 403 |
| Chain | Residue |
| A | SER244 |
| A | GLN245 |
| A | SER289 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 404 |
| Chain | Residue |
| A | LEU312 |
| A | LYS335 |
| A | ASP336 |
| A | GLY337 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue FMT B 401 |
| Chain | Residue |
| A | LYS150 |
| A | GLY151 |
| B | LYS320 |
| B | VAL321 |
| B | THR322 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue ACT B 402 |
| Chain | Residue |
| B | ASN74 |
| B | VAL78 |
| B | HOH662 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue FMT B 403 |
| Chain | Residue |
| B | GLY126 |
| B | THR145 |
| B | GLU146 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | binding site for residue CIT B 404 |
| Chain | Residue |
| B | HIS235 |
| B | LEU246 |
| B | GLY247 |
| B | GLY248 |
| B | HIS250 |
| B | LYS290 |
| B | THR341 |
| B | TYR343 |
| B | HOH604 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue ACT B 405 |
| Chain | Residue |
| B | TYR226 |
| B | LYS308 |
| site_id | AD1 |
| Number of Residues | 1 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | GLU45 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue FMT B 407 |
| Chain | Residue |
| B | GLU229 |
| B | GLY337 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 120 |
| Details | Domain: {"description":"Nsp15 N-terminal oligomerization","evidences":[{"source":"PROSITE-ProRule","id":"PRU01305","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 250 |
| Details | Domain: {"description":"AV-Nsp11N/CoV-Nsp15M","evidences":[{"source":"PROSITE-ProRule","id":"PRU01306","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 278 |
| Details | Domain: {"description":"NendoU","evidences":[{"source":"PROSITE-ProRule","id":"PRU01303","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor; for uridylate-specific endoribonuclease nsp15 activity","evidences":[{"source":"PubMed","id":"33504779","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33564093","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor; for uridylate-specific endoribonuclease nsp15 activity","evidences":[{"source":"PubMed","id":"33504779","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33564093","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Active site: {"description":"For uridylate-specific endoribonuclease nsp15 activity","evidences":[{"source":"PubMed","id":"33504779","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"33504779","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33564093","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"33564093","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Site: {"description":"Transition state stabilizer","evidences":[{"source":"PubMed","id":"33504779","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33564093","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Site: {"description":"Uracil recognition site","evidences":[{"source":"PubMed","id":"33504779","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"33564093","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
