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Crystal structure of dengue 1 virus envelope glycoprotein
Analyse Crystal structure of dengue 1 virus envelope glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A3R
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- B1N6C5
- Ligands
- NAG, FUC
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 379 | 7% helix, 48% strand | B1N6C5 |
| B | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 383 | 6% helix, 44% strand | B1N6C5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.65 | 0.85 | 24 | empty |
| 2 | 377 | 0.64 | 0.79 | 51 | empty |
| 3 | 274 | 0.53 | 0.76 | 33 | empty |
| 4 | 117 | 0.49 | 0.80 | 21 | empty |
| 5 | 153 | 0.44 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1597 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7A3R · Crystal structure of dengue 1 virus envelope glycoprotein · 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 B1N6C5
- Elsewhere: RCSB PDB 7A3R · PDBe 7A3R · UniProt B1N6C5
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