MolNFT v1 · #89675 · protein
Crystal structure of the glycoprotein erns from the pestivirus bvdv-1 in complex with zn ions
4DWC · E(RNS) glycoprotein: “Crystal structure of the glycoprotein erns from the pestivirus bvdv-1 in complex with zn ions”. X-ray diffraction, 6 ligands (NAG, BMA, MAN), 3 pockets (best druggability 0.64). MolNFT v1 #89675 on GenesisL1…
- PDB
- 4DWC
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E(RNS) glycoprotein
- UniProt
- Q96662
- Ligands
- NAG, BMA, MAN, FCA, ZN, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E(RNS) glycoprotein | protein | 158 | 28% helix, 25% strand | Q96662 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- FCA · alpha-D-fucopyranose · sugar · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.64 | 0.79 | 43 | ZN, SO4 |
| 2 | 213 | 0.46 | 0.74 | 34 | ZN |
| 3 | 56 | 0.39 | 0.80 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 490 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DWC · Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with Zn… · 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 4DWC · PDBe 4DWC · UniProt Q96662
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