Research workbench
Structure of the tetragonal crystal form of X (adrp) domain from fcov
Analyse Structure of the tetragonal crystal form of X (adrp) domain from fcov in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EW5
- Type
- protein
- Length
- 502 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macro domain of non-structural protein 3
- UniProt
- Q98VG9
- Ligands
- 1GP, SO4, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Macro domain of non-structural protein 3 | protein | 168 | 36% helix, 22% strand | Q98VG9 |
| B | Macro domain of non-structural protein 3 | protein | 166 | 39% helix, 23% strand | Q98VG9 |
Ligands and binding sites
- 1GP · Sn-glycerol-1-phosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.68 | 0.85 | 35 | 1GP |
| 2 | 366 | 0.66 | 0.80 | 53 | empty |
| 3 | 163 | 0.60 | 0.83 | 31 | 1GP |
| 4 | 129 | 0.57 | 0.83 | 24 | 1GP |
| 5 | 57 | 0.27 | 0.73 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 485 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 469 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3EW5 · Structure of the tetragonal crystal form of X (ADRP) domain from FCoV · 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 Q98VG9
- Elsewhere: RCSB PDB 3EW5 · PDBe 3EW5 · UniProt Q98VG9
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