Research workbench
Cryo-EM structure of SARS-cov-2 NSP15 nendou at pH 7.5
Analyse Cryo-EM structure of SARS-cov-2 NSP15 nendou at pH 7.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RB0
- Type
- protein
- Length
- 2,082 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate-specific endoribonuclease
- EC
- 3.1.-.-
- UniProt
- P0DTD1
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, A, B, C | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 22% helix, 29% strand | P0DTD1 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.88 | 0.89 | 147 | empty |
| 2 | 447 | 0.68 | 0.79 | 53 | empty |
| 3 | 414 | 0.67 | 0.80 | 53 | empty |
| 4 | 418 | 0.66 | 0.79 | 54 | empty |
| 5 | 260 | 0.65 | 0.82 | 42 | empty |
Interfaces
15 interfaces between chains.
- D–F · 1016 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 1012 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1009 Ų buried · 8 hydrogen bonds · protein-protein
- E–A · 1008 Ų buried · 7 hydrogen bonds · protein-protein
- F–B · 1008 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7RB0 · Cryo-EM structure of SARS-CoV-2 NSP15 NendoU at pH 7.5 · the same entry in another collection · chain D against D, 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 7RB0 · PDBe 7RB0 · UniProt P0DTD1
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