Research workbench
West nile virus in complex with Fab fragments of mab CR4354 (fitted coordinates of envelope proteins and Fab fragments of one icosahedral asu)
Analyse West nile virus in complex with Fab fragments of mab CR4354 (fitted coordinates… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IYW
- Type
- protein
- Length
- 2,100 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein; CR4354 Fab fragment X1, heavy chain H; CR4354 Fab fragment X1, light chain L
- UniProt
- Q9Q6P4
- Ligands
- NDG, FUL
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Polyprotein | protein | 400 | 7% helix, 41% strand | Q9Q6P4 |
| H, K | CR4354 Fab fragment X1, heavy chain H | protein | 230 | 7% helix, 49% strand | — |
| L, M | CR4354 Fab fragment X1, light chain L | protein | 220 | 6% helix, 50% strand | — |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains A, B, C
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 | 1136 | 0.82 | 0.83 | 112 | empty |
| 2 | 837 | 0.71 | 0.76 | 84 | empty |
| 3 | 632 | 0.69 | 0.78 | 60 | empty |
| 4 | 104 | 0.60 | 0.86 | 22 | empty |
| 5 | 160 | 0.59 | 0.82 | 31 | empty |
Interfaces
12 interfaces between chains.
- K–M · 1739 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1738 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1470 Ų buried · 29 hydrogen bonds · protein-protein
- C–K · 848 Ų buried · 33 hydrogen bonds · protein-protein
- A–H · 838 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 3IYW · West Nile virus in complex with Fab fragments of MAb CR4354 (fitted coordinates of… · the same entry in another collection · chain B against B, 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 Q9Q6P4
- Elsewhere: RCSB PDB 3IYW · PDBe 3IYW · UniProt Q9Q6P4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.