MolNFT v1 · #179309 · protein
Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with uridine-2',3'-vanadate
7K1L · Uridylate-specific endoribonuclease: “Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with uridine-2',3'-vanadate”. X-ray diffraction, 2 ligands (UVC, SO4), 5 pockets (best druggability 0.58). MolNFT v1…
- PDB
- 7K1L
- Type
- protein
- Length
- 694 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
- UVC, SO4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 22% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- UVC · Uridine-2',3'-vanadate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.58 | 0.80 | 27 | empty |
| 2 | 180 | 0.54 | 0.79 | 27 | empty |
| 3 | 289 | 0.51 | 0.74 | 32 | empty |
| 4 | 79 | 0.32 | 0.74 | 16 | EDO |
| 5 | 55 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 75 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K1L · 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 7K1L · PDBe 7K1L · UniProt P0DTD1
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