MolNFT v1 · #109482 · protein
Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3
4X42 · Envelope protein E: “Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.72). MolNFT v1 #109482 on GenesisL1: 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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