Research workbench
Nucleotide bound SARS-cov-2 NSP15
Analyse Nucleotide bound SARS-cov-2 NSP15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K0R
- Type
- protein
- Length
- 2,070 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Ligands
- U5P, PO4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 345 | 21% helix, 32% strand | P0DTD1 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.84 | 0.85 | 112 | empty |
| 2 | 1027 | 0.75 | 0.78 | 102 | empty |
| 3 | 1062 | 0.75 | 0.77 | 100 | empty |
| 4 | 387 | 0.64 | 0.78 | 40 | empty |
| 5 | 384 | 0.63 | 0.78 | 41 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1035 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1027 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1006 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1006 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 999 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7K0R · Nucleotide bound SARS-CoV-2 Nsp15 · 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 7K0R · PDBe 7K0R · UniProt P0DTD1
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