Research workbench
Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP14 in complex with Z2856434807
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
- 5SM5
- Type
- protein
- Length
- 459 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proofreading exoribonuclease NSP14
- EC
- 3.1.13.-
- UniProt
- P0DTD1
- Ligands
- S5J, ZN, PO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Proofreading exoribonuclease NSP14 (EC 3.1.13.-) | protein | 459 | 30% helix, 21% strand | P0DTD1 |
Ligands and binding sites
- S5J · 2-[4-(2-methoxyphenyl)piperazin-1-yl]ethanenitrile · 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 | 0.69 | 0.81 | 33 | empty |
| 2 | 205 | 0.50 | 0.76 | 34 | empty |
| 3 | 55 | 0.33 | 0.78 | 22 | PO4 |
| 4 | 65 | 0.30 | 0.74 | 17 | empty |
| 5 | 64 | 0.30 | 0.74 | 14 | PO4 |
Compared structures
- 5SM5 · 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 5SM5 · PDBe 5SM5 · UniProt P0DTD1
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