Research workbench
Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with uridine-3',5'-diphosphate
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
- 7K1O
- Type
- protein
- Length
- 1,040 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- VQV
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 346 | 22% helix, 32% strand | P0DTD1 |
| B, C | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 21% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- VQV · 1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.65 | 0.78 | 40 | empty |
| 2 | 225 | 0.59 | 0.80 | 28 | empty |
| 3 | 203 | 0.56 | 0.80 | 24 | empty |
| 4 | 200 | 0.53 | 0.78 | 37 | empty |
| 5 | 188 | 0.48 | 0.76 | 44 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 1202 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 34 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K1O · 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 7K1O · PDBe 7K1O · UniProt P0DTD1
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