Research workbench
Crystal structure of the glycoprotein erns from the pestivirus bvdv-1 in complex with 5'-cmp
Analyse Crystal structure of the glycoprotein erns from the pestivirus bvdv-1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DW3
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E(RNS) glycoprotein
- UniProt
- Q96662
- Ligands
- C5P, NAG, BMA, MAN, SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E(RNS) glycoprotein | protein | 161 | 29% helix, 24% strand | Q96662 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.63 | 0.77 | 47 | C5P |
| 2 | 206 | 0.45 | 0.74 | 37 | C5P |
| 3 | 67 | 0.32 | 0.75 | 12 | empty |
| 4 | 62 | 0.30 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 504 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DW3 · Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with… · 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 Q96662
- Elsewhere: RCSB PDB 4DW3 · PDBe 4DW3 · UniProt Q96662
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