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PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in complex with Z71580604
Analyse PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NSP14 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SMI
- Type
- protein
- Length
- 459 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.08
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Proofreading exoribonuclease nsp14
- EC
- 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- LQV, ZN, PO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.08 · 1 distinct chain · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Proofreading exoribonuclease nsp14 (EC 3.1.13.-) | protein | 459 | 29% helix, 21% strand | P0DTD1 |
Ligands and binding sites
- LQV · (2S)-N-(5-methylpyridin-2-yl)oxolane-2-carboxamide · ligand · chains D
- ZN · Zinc ion · metal · 3 copies · chains D
- PO4 · Phosphate ion · ion · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.68 | 0.80 | 33 | empty |
| 2 | 178 | 0.47 | 0.76 | 29 | empty |
| 3 | 72 | 0.39 | 0.79 | 20 | PO4 |
| 4 | 77 | 0.30 | 0.74 | 17 | empty |
| 5 | 53 | 0.30 | 0.76 | 13 | empty |
Compared structures
- 5SMI · Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP14 in complex with… · 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 5SMI · PDBe 5SMI · UniProt P0DTD1
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