Research workbench
Structure of NSP14 from SARS-cov-2 in complex with sah
Analyse Structure of NSP14 from SARS-cov-2 in complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R2V
- Type
- protein
- Length
- 879 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proofreading exoribonuclease NSP14
- EC
- 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- SAH, ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proofreading exoribonuclease NSP14 (EC 3.1.13.-) | protein | 440 | 32% helix, 21% strand | P0DTD1 |
| B | Proofreading exoribonuclease NSP14 (EC 3.1.13.-) | protein | 439 | 31% helix, 21% strand | P0DTD1 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.83 | 0.84 | 79 | PEG |
| 2 | 659 | 0.75 | 0.81 | 58 | SAH, PEG |
| 3 | 632 | 0.75 | 0.81 | 50 | SAH, PEG |
| 4 | 89 | 0.45 | 0.79 | 16 | empty |
| 5 | 146 | 0.45 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7R2V · Structure of nsp14 from SARS-CoV-2 in complex with SAH · 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 7R2V · PDBe 7R2V · UniProt P0DTD1
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