MolNFT v1 · #89653 · protein
Crystal structure of the glycoprotein erns from the pestivirus bvdv-1 in complex with 2'-ump
4DVN · E(RNS) glycoprotein: “Crystal structure of the glycoprotein erns from the pestivirus bvdv-1 in complex with 2'-ump”. X-ray diffraction, 5 ligands (U2P, NAG, BMA), 4 pockets (best druggability 0.62). MolNFT v1 #89653 on GenesisL1: 3D…
- PDB
- 4DVN
- 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
- U2P, NAG, BMA, MAN, SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E(RNS) glycoprotein | protein | 161 | 29% helix, 23% strand | Q96662 |
Ligands and binding sites
- U2P · Phosphoric acid mono-[2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-hydroxymethyl-tetrahydro-furan-3-yl] ester · ligand · 3 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 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
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 | 358 | 0.62 | 0.78 | 50 | SO4 |
| 2 | 225 | 0.45 | 0.73 | 40 | U2P |
| 3 | 83 | 0.34 | 0.75 | 14 | empty |
| 4 | 65 | 0.31 | 0.75 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 530 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DVN · 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 4DVN · PDBe 4DVN · UniProt Q96662
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.