Research workbench
Crystal structure of DENV1-E111 Fab fragment bound to denv-1 diii (western pacific-74 strain).
Analyse Crystal structure of DENV1-E111 Fab fragment bound to denv-1 diii (western… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FFZ
- Type
- protein
- Length
- 1,060 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope protein E; DENV1-E111 Fab fragment (light chain); DENV1-E111 Fab fragment (heavy…
- UniProt
- P17763
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, X | Envelope protein E | protein | 97 | 0% helix, 47% strand | P17763 |
| L, Y | DENV1-E111 Fab fragment (light chain) | protein | 216 | 6% helix, 56% strand | — |
| H, Z | DENV1-E111 Fab fragment (heavy chain) | protein | 217 | 4% helix, 51% strand | — |
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.65 | 0.75 | 62 | empty |
| 2 | 454 | 0.58 | 0.74 | 56 | empty |
| 3 | 238 | 0.49 | 0.75 | 28 | empty |
| 4 | 115 | 0.44 | 0.78 | 19 | empty |
| 5 | 118 | 0.44 | 0.77 | 18 | empty |
Interfaces
8 interfaces between chains.
- Y–Z · 1866 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1862 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 593 Ų buried · 6 hydrogen bonds · protein-protein
- X–Z · 592 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 561 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4FFZ · Crystal Structure of DENV1-E111 fab fragment bound to DENV-1 DIII (Western Pacific-74… · 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 P17763
- Elsewhere: RCSB PDB 4FFZ · PDBe 4FFZ · UniProt P17763
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