Research workbench
Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3
Analyse Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X42
- Type
- protein
- Length
- 594 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E
- UniProt
- P09866
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope protein E | protein | 99 | 0% helix, 47% strand | P09866 |
| B, F | Envelope protein E | protein | 100 | 0% helix, 47% strand | P09866 |
| C | Envelope protein E | protein | 97 | 0% helix, 48% strand | P09866 |
| D | Envelope protein E | protein | 102 | 0% helix, 48% strand | P09866 |
| E | Envelope protein E | protein | 96 | 0% helix, 49% strand | P09866 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.72 | 0.78 | 63 | SO4 |
| 2 | 612 | 0.71 | 0.78 | 50 | SO4 |
| 3 | 341 | 0.64 | 0.80 | 41 | empty |
| 4 | 88 | 0.42 | 0.79 | 27 | empty |
| 5 | 114 | 0.42 | 0.77 | 26 | empty |
Interfaces
7 interfaces between chains.
- C–D · 693 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 497 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4X42 · Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3 · 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 P09866
- Elsewhere: RCSB PDB 4X42 · PDBe 4X42 · UniProt P09866
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