Research workbench
DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scFv)
Analyse DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K93
- Type
- protein
- Length
- 2,244 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.89
- Source
- Dengue virus 2; Mus musculus
- Molecule
- Non-structural protein 1; 2B7 single chain fab variable region
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- D0EPS0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.89 · 6 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 327 | 17% helix, 32% strand | D0EPS0 |
| B | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 328 | 17% helix, 34% strand | D0EPS0 |
| C | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 335 | 17% helix, 33% strand | D0EPS0 |
| D | Non-structural protein 1 (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 325 | 17% helix, 35% strand | D0EPS0 |
| E | 2B7 single chain fab variable region | protein | 233 | 4% helix, 48% strand | — |
| G, I, K | 2B7 single chain fab variable region | protein | 232 | 4% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.77 | 0.79 | 110 | empty |
| 2 | 519 | 0.75 | 0.83 | 45 | empty |
| 3 | 117 | 0.74 | 0.94 | 24 | empty |
| 4 | 571 | 0.72 | 0.80 | 40 | empty |
| 5 | 127 | 0.71 | 0.92 | 29 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2826 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2817 Ų buried · 47 hydrogen bonds · protein-protein
- A–E · 707 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 694 Ų buried · 9 hydrogen bonds · protein-protein
- D–K · 682 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7K93 · DENV2 NS1 in complex with neutralizing 2B7 single chain Fab variable region (scfv) · 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 D0EPS0
- Elsewhere: RCSB PDB 7K93 · PDBe 7K93 · UniProt D0EPS0
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