Research workbench
Cryo-EM structure of SARS-cov-2 NSP15 nendou in bis-tris pH 6.0
Analyse Cryo-EM structure of SARS-cov-2 NSP15 nendou in bis-tris pH 6.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RB2
- 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 0.84
Structure
electron microscopy · 1 distinct chain · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Uridylate-specific endoribonuclease (EC 3.1.-.-) | protein | 347 | 21% 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 | 815 | 0.84 | 0.87 | 104 | empty |
| 2 | 536 | 0.70 | 0.79 | 60 | empty |
| 3 | 488 | 0.70 | 0.80 | 52 | empty |
| 4 | 519 | 0.70 | 0.79 | 60 | empty |
| 5 | 496 | 0.69 | 0.79 | 57 | empty |
Interfaces
15 interfaces between chains.
- B–F · 1058 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1046 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 1045 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 1040 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1037 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7RB2 · Cryo-EM structure of SARS-CoV-2 NSP15 NendoU in BIS-Tris pH 6.0 · 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 7RB2 · PDBe 7RB2 · UniProt P0DTD1
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