MolNFT v1 · #168386 · protein
DENV2 NS1 in complex with neutralizing 2B7 Fab fragment
6WER · Non-structural protein 1: “DENV2 NS1 in complex with neutralizing 2B7 Fab fragment”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.75). MolNFT v1 #168386 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WER
- Type
- protein
- Length
- 1,506 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 1; 2B7 Fab heavy chain; 2B7 Fab light chain
- UniProt
- D0EPS0
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 1 | protein | 322 | 16% helix, 33% strand | D0EPS0 |
| B | Non-structural protein 1 | protein | 324 | 18% helix, 33% strand | D0EPS0 |
| C, E | 2B7 Fab heavy chain | protein | 215 | 3% helix, 49% strand | — |
| D, F | 2B7 Fab light chain | protein | 215 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.75 | 0.95 | 25 | empty |
| 2 | 53 | 0.69 | 0.97 | 20 | empty |
| 3 | 595 | 0.64 | 0.75 | 60 | empty |
| 4 | 259 | 0.63 | 0.81 | 48 | empty |
| 5 | 563 | 0.62 | 0.74 | 55 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2232 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 1918 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1897 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 488 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6WER · DENV2 NS1 in complex with neutralizing 2B7 Fab fragment · 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 6WER · PDBe 6WER · UniProt D0EPS0
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