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Crystal structure of dengue 3 virus envelope glycoprotein
Analyse Crystal structure of dengue 3 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
- 7A3S
- Type
- protein
- Length
- 1,149 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- P27915
- Ligands
- NAG, SO4
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 384 | 7% helix, 49% strand | P27915 |
| B | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 383 | 7% helix, 50% strand | P27915 |
| C | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 382 | 7% helix, 49% strand | P27915 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.68 | 0.77 | 63 | empty |
| 2 | 466 | 0.64 | 0.77 | 43 | empty |
| 3 | 291 | 0.52 | 0.75 | 26 | SO4 |
| 4 | 206 | 0.52 | 0.77 | 26 | empty |
| 5 | 99 | 0.46 | 0.80 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1599 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 762 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7A3S · Crystal structure of dengue 3 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 P27915
- Elsewhere: RCSB PDB 7A3S · PDBe 7A3S · UniProt P27915
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