MolNFT v1 · #167834 · protein
Crystal structure of NSP15 endoribonuclease from SARS cov-2.
6VWW · Uridylate-specific endoribonuclease: “Crystal structure of NSP15 endoribonuclease from SARS cov-2.”. X-ray diffraction, 2 ligands (MG, CL), 6 pockets (best druggability 0.59). MolNFT v1 #167834 on GenesisL1: 3D structure, binding…
- PDB
- 6VWW
- 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
- MG, CL
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 348 | 21% helix, 30% strand | P0DTD1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 9 copies · chains A, B
- ACY · Acetic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.59 | 0.81 | 28 | GOL |
| 2 | 217 | 0.57 | 0.79 | 25 | GOL, ACY |
| 3 | 365 | 0.56 | 0.74 | 38 | empty |
| 4 | 120 | 0.43 | 0.77 | 18 | empty |
| 5 | 70 | 0.36 | 0.77 | 16 | GOL |
Interfaces
1 interface between chains.
- A–B · 144 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VWW · Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2. · 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 6VWW · PDBe 6VWW · UniProt P0DTD1
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