Research workbench
Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with uridine-5'-monophosphate
Analyse Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WLC
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- U5P, SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 21% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.59 | 0.79 | 34 | empty |
| 2 | 219 | 0.58 | 0.80 | 25 | EDO |
| 3 | 164 | 0.41 | 0.72 | 28 | empty |
| 4 | 98 | 0.37 | 0.75 | 19 | empty |
| 5 | 60 | 0.27 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WLC · Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 6WLC · PDBe 6WLC · UniProt P0DTD1
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