6W01
The 1.9 A Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with a Citrate
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 401 |
| Chain | Residue |
| A | LEU43 |
| A | PHE44 |
| A | GLU45 |
| A | TRP59 |
| A | HOH506 |
| A | HOH573 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 402 |
| Chain | Residue |
| B | ASN53 |
| B | GLU57 |
| B | CYS103 |
| B | SER104 |
| B | MET105 |
| A | GLU4 |
| A | PRO24 |
| A | VAL25 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 403 |
| Chain | Residue |
| A | ILE169 |
| A | GLY170 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | LEU312 |
| A | SER313 |
| A | VAL314 |
| A | CYS334 |
| A | LYS335 |
| A | ASP336 |
| A | GLY337 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue PEG A 405 |
| Chain | Residue |
| A | HIS250 |
| A | ASN278 |
| A | VAL292 |
| A | CYS293 |
| A | SER294 |
| A | CIT412 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue PEG A 406 |
| Chain | Residue |
| A | ASN75 |
| A | LEU76 |
| A | GLY77 |
| A | LYS181 |
| A | PRO191 |
| A | TYR325 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | ASN74 |
| A | GLY77 |
| A | VAL78 |
| A | ASP79 |
| A | HOH564 |
| A | HOH588 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | GLU229 |
| A | GLY230 |
| A | TYR231 |
| A | GLY337 |
| A | HIS338 |
| A | HOH747 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | ARG199 |
| A | ASN200 |
| A | LEU201 |
| A | HOH670 |
| site_id | AD1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 410 |
| Chain | Residue |
| A | TYR226 |
| A | LYS308 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 411 |
| Chain | Residue |
| A | GLU305 |
| A | HOH592 |
| B | ARG136 |
| site_id | AD3 |
| Number of Residues | 12 |
| Details | binding site for residue CIT A 412 |
| Chain | Residue |
| A | HIS235 |
| A | GLN245 |
| A | LEU246 |
| A | GLY247 |
| A | GLY248 |
| A | HIS250 |
| A | LYS290 |
| A | THR341 |
| A | TYR343 |
| A | PEG405 |
| A | HOH627 |
| A | HOH700 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 413 |
| Chain | Residue |
| A | PRO158 |
| A | LYS159 |
| A | GLN160 |
| A | GLN197 |
| site_id | AD5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 414 |
| Chain | Residue |
| A | VAL156 |
| A | GLU192 |
| A | THR193 |
| A | PHE195 |
| A | HOH678 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 401 |
| Chain | Residue |
| B | PHE44 |
| B | TRP59 |
| B | HOH502 |
| B | HOH516 |
| B | HOH561 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 402 |
| Chain | Residue |
| A | ASN53 |
| A | GLU57 |
| A | CYS103 |
| A | SER104 |
| A | MET105 |
| B | GLU4 |
| B | PRO24 |
| B | VAL25 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 403 |
| Chain | Residue |
| B | SER274 |
| B | THR275 |
| B | VAL276 |
| B | ILE328 |
| B | HOH605 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 404 |
| Chain | Residue |
| B | HOH674 |
| B | ASN74 |
| B | GLY77 |
| B | VAL78 |
| B | ASP79 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| A | PRO191 |
| A | GLU327 |
| B | SER148 |
| B | HOH679 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | GLU146 |
| B | VAL156 |
| B | LYS174 |
| B | GLN176 |
| B | ASN178 |
| site_id | AE3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | LYS159 |
| B | GLN160 |
| B | GLN197 |
| site_id | AE4 |
| Number of Residues | 10 |
| Details | binding site for residue CIT B 408 |
| Chain | Residue |
| B | HIS235 |
| B | GLN245 |
| B | LEU246 |
| B | GLY247 |
| B | GLY248 |
| B | HIS250 |
| B | LYS290 |
| B | THR341 |
| B | TYR343 |
| B | HOH670 |
| site_id | AE5 |
| Number of Residues | 9 |
| Details | binding site for residue EDO B 409 |
| Chain | Residue |
| A | LYS320 |
| A | VAL321 |
| A | THR322 |
| A | GLU327 |
| B | VAL149 |
| B | LYS150 |
| B | GLY151 |
| B | LEU152 |
| B | HOH591 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 410 |
| Chain | Residue |
| B | SER155 |
| B | VAL156 |
| B | GLU192 |
| B | THR193 |
| B | PHE195 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue PEG B 411 |
| Chain | Residue |
| B | ASN75 |
| B | LEU76 |
| B | GLY77 |
| B | LYS181 |
| site_id | AE8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 412 |
| Chain | Residue |
| B | GLU192 |
| B | VAL321 |
| B | THR322 |
| B | HOH515 |
| site_id | AE9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 413 |
| Chain | Residue |
| A | GLU192 |
| B | THR145 |
| B | GLY147 |
| B | SER148 |
| B | HOH517 |
| B | HOH611 |
| B | HOH689 |
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":"Cleavage; by 3CL-PRO","evidences":[{"source":"UniProtKB","id":"P0C6V3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| 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_FI11 |
| 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 |
