Research workbench
West nile virus NS1 in complex with neutralizing 22NS1 antibody Fab
Analyse West nile virus NS1 in complex with neutralizing 22NS1 antibody Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OII
- Type
- protein
- Length
- 1,214 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein NS1; Light chain of Fab fragment of 22NS1 antibody; Heavy chain of…
- UniProt
- U3N977
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-structural protein NS1 | protein | 177 | 5% helix, 32% strand | U3N977 |
| L, M | Light chain of Fab fragment of 22NS1 antibody | protein | 213 | 7% helix, 54% strand | — |
| H, I | Heavy chain of Fab fragment of 22NS1 antibody | protein | 217 | 6% helix, 54% strand | — |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.76 | 0.78 | 105 | empty |
| 2 | 166 | 0.71 | 0.90 | 28 | empty |
| 3 | 450 | 0.58 | 0.74 | 62 | empty |
| 4 | 402 | 0.56 | 0.74 | 55 | empty |
| 5 | 99 | 0.48 | 0.81 | 21 | empty |
Interfaces
12 interfaces between chains.
- L–H · 1817 Ų buried · 9 hydrogen bonds · protein-protein
- M–I · 1810 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 761 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 714 Ų buried · 13 hydrogen bonds · protein-protein
- B–I · 678 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4OII · West Nile Virus NS1 in complex with neutralizing 22NS1 antibody Fab · 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 U3N977
- Elsewhere: RCSB PDB 4OII · PDBe 4OII · UniProt U3N977
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