Research workbench
Crystal structure of an active-site mutant of the glycoprotein erns from the pestivirus bvdv-1 in complex with a cpupc trinucleotide
Analyse Crystal structure of an active-site mutant of the glycoprotein erns from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DWA
- Type
- protein + RNA
- Length
- 313 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E(RNS) glycoprotein; RNA (5'-R(*CP*UP*C)-3')
- UniProt
- Q96662
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E(RNS) glycoprotein | protein | 154 | 30% helix, 25% strand | Q96662 |
| B | E(RNS) glycoprotein | protein | 156 | 31% helix, 24% strand | Q96662 |
| D | RNA (5'-R(*CP*UP*C)-3') | rna | 3 | — | — |
Ligands and binding sites
- 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 · chains B
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.67 | 0.77 | 51 | SO4 |
| 2 | 337 | 0.60 | 0.78 | 44 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 555 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 270 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 38 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 9 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 4DWA · Crystal structure of an active-site mutant of the glycoprotein Erns from the pestivirus… · 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 4DWA · PDBe 4DWA · UniProt Q96662
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