Research workbench
Crystal structure of DENV1-E111 single chain variable fragment bound to denv-1 diii, strain 16007.
Analyse Crystal structure of DENV1-E111 single chain variable fragment bound to denv-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FFY
- Type
- protein
- Length
- 328 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DENV1-E111 single chain variable fragment (light chain); DENV1-E111 single chain variable…
- UniProt
- Q9J7C6
- Ligands
- CL, SO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | DENV1-E111 single chain variable fragment (light chain) | protein | 112 | 3% helix, 54% strand | — |
| H | DENV1-E111 single chain variable fragment (heavy chain) | protein | 119 | 5% helix, 52% strand | — |
| A | Envelope glycoprotein | protein | 97 | 0% helix, 47% strand | Q9J7C6 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains L, H
- SO4 · Sulfate ion · ion · chains H, A
- GOL · Glycerol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.40 | 0.78 | 14 | empty |
| 2 | 65 | 0.28 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 851 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 586 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 567 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4FFY · Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII… · the same entry in another collection · chain L against L, 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 Q9J7C6
- Elsewhere: RCSB PDB 4FFY · PDBe 4FFY · UniProt Q9J7C6
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