MolNFT v1 · #169218 · protein
Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with 3'-uridinemonophosphate
6X4I · Uridylate-specific endoribonuclease: “Crystal structure of NSP15 endoribonuclease from SARS cov-2 in the complex with 3'-uridinemonophosphate”. X-ray diffraction, 2 ligands (U3P, NA), 8 pockets (best druggability 0.58). MolNFT v1…
- PDB
- 6X4I
- Type
- protein
- Length
- 695 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
- U3P, NA
- Pockets
- 8 · best druggability 0.58
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 | 348 | 21% helix, 31% strand | P0DTD1 |
| B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 21% helix, 31% strand | P0DTD1 |
Ligands and binding sites
- U3P · 3'-uridinemonophosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.58 | 0.81 | 26 | empty |
| 2 | 191 | 0.56 | 0.80 | 23 | empty |
| 3 | 128 | 0.38 | 0.73 | 17 | empty |
| 4 | 83 | 0.34 | 0.74 | 16 | empty |
| 5 | 81 | 0.33 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6X4I · 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 6X4I · PDBe 6X4I · UniProt P0DTD1
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