Research workbench
Structure of the C-terminal domain of NSP4 from feline coronavirus
Analyse Structure of the C-terminal domain of NSP4 from feline coronavirus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZF
- Type
- protein
- Length
- 456 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicase polyprotein 1AB
- UniProt
- Q98VG9
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.46
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicase polyprotein 1AB | protein | 96 | 51% helix, 16% strand | Q98VG9 |
| B | Replicase polyprotein 1AB | protein | 93 | 47% helix, 16% strand | Q98VG9 |
| C | Replicase polyprotein 1AB | protein | 92 | 50% helix, 17% strand | Q98VG9 |
| D | Replicase polyprotein 1AB | protein | 91 | 51% helix, 18% strand | Q98VG9 |
| E | Replicase polyprotein 1AB | protein | 84 | 57% helix, 12% strand | Q98VG9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.46 | 0.77 | 28 | empty |
| 2 | 81 | 0.44 | 0.80 | 18 | SO4 |
| 3 | 73 | 0.44 | 0.81 | 18 | empty |
| 4 | 129 | 0.43 | 0.76 | 23 | empty |
| 5 | 108 | 0.39 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1000 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 999 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 489 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 477 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 169 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3GZF · Structure of the C-terminal domain of nsp4 from Feline Coronavirus · 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 3GZF · PDBe 3GZF · UniProt Q98VG9
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