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Structural mimicry of the dengue virus envelope glycoprotein revealed by the crystallographic study of an idiotype-anti-idiotype Fab complex.
Analyse Structural mimicry of the dengue virus envelope glycoprotein revealed by the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XAJ
- Type
- protein
- Length
- 1,736 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FABHM14C10 heavy chain; FABHM14C10 light chain; Fab E1 light chain; Fab E1 heavy chain
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FABHM14C10 heavy chain | protein | 226 | 6% helix, 50% strand | — |
| B, L | FABHM14C10 light chain | protein | 214 | 5% helix, 50% strand | — |
| C | Fab E1 light chain | protein | 214 | 8% helix, 49% strand | — |
| D | Fab E1 light chain | protein | 213 | 8% helix, 49% strand | — |
| E | Fab E1 heavy chain | protein | 215 | 6% helix, 49% strand | — |
| F | Fab E1 heavy chain | protein | 213 | 6% helix, 49% strand | — |
| H | FABHM14C10 heavy chain | protein | 227 | 6% helix, 52% strand | — |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.73 | 0.86 | 34 | empty |
| 2 | 931 | 0.71 | 0.76 | 113 | empty |
| 3 | 968 | 0.71 | 0.75 | 119 | empty |
| 4 | 257 | 0.69 | 0.85 | 34 | empty |
| 5 | 200 | 0.64 | 0.83 | 27 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2076 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 2075 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1561 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 1515 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 488 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 5XAJ · Structural mimicry of the dengue virus envelope glycoprotein revealed by the… · 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
- Elsewhere: RCSB PDB 5XAJ · PDBe 5XAJ
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