Research workbench
DENV1 NS1 in complex with neutralizing 2B7 Fab fragment
Analyse DENV1 NS1 in complex with neutralizing 2B7 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WEQ
- Type
- protein
- Length
- 3,073 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 1; 2B7 Fab fragment heavy chain; 2B7 Fab fragment light chain
- UniProt
- Q9J7C6
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Non-structural protein 1 | protein | 340 | 17% helix, 35% strand | Q9J7C6 |
| E | 2B7 Fab fragment heavy chain | protein | 214 | 4% helix, 50% strand | — |
| F, H, J, L | 2B7 Fab fragment light chain | protein | 215 | 7% helix, 55% strand | — |
| G, I, K | 2B7 Fab fragment heavy chain | protein | 213 | 3% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.80 | 0.82 | 99 | empty |
| 2 | 531 | 0.75 | 0.83 | 42 | empty |
| 3 | 961 | 0.74 | 0.77 | 82 | empty |
| 4 | 853 | 0.73 | 0.77 | 90 | empty |
| 5 | 55 | 0.72 | 0.98 | 20 | empty |
Interfaces
30 interfaces between chains.
- C–D · 3132 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3111 Ų buried · 66 hydrogen bonds · protein-protein
- E–F · 1963 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 1897 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1892 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6WEQ · DENV1 NS1 in complex with neutralizing 2B7 Fab fragment · the same entry in another collection · chain D against D, 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 6WEQ · PDBe 6WEQ · UniProt Q9J7C6
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