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Crystal structure of Fab 1A1D-2 complexed with E-diii of dengue virus at 3.8 ångström resolution
Analyse Crystal structure of Fab 1A1D-2 complexed with E-diii of dengue virus at 3.8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R69
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major envelope protein E; Heavy chain of 1A1D-2; Light chain of 1A1D-2
- UniProt
- P18356
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major envelope protein E | protein | 97 | 0% helix, 33% strand | P18356 |
| H | Heavy chain of 1A1D-2 | protein | 203 | 3% helix, 32% strand | — |
| L | Light chain of 1A1D-2 | protein | 204 | 0% helix, 26% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.65 | 0.82 | 39 | empty |
| 2 | 620 | 0.62 | 0.74 | 67 | empty |
| 3 | 53 | 0.39 | 0.81 | 16 | empty |
| 4 | 67 | 0.38 | 0.79 | 15 | empty |
| 5 | 68 | 0.35 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1827 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 486 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 477 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2R69 · Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom… · 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 P18356
- Elsewhere: RCSB PDB 2R69 · PDBe 2R69 · UniProt P18356
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