Research workbench
Structure of MEDI8852 Fab fragment in complex with H7 ha
Analyse Structure of MEDI8852 Fab fragment in complex with H7 ha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JW3
- Type
- protein
- Length
- 914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; MEDI8852 heavy chain; MEDI8852 light chain
- UniProt
- Q701U0
- Ligands
- NAG, BMA, MAN
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 316 | 9% helix, 40% strand | Q701U0 |
| B | Hemagglutinin | protein | 170 | 51% helix, 15% strand | Q701U0 |
| H | MEDI8852 heavy chain | protein | 222 | 6% helix, 54% strand | — |
| L | MEDI8852 light chain | protein | 206 | 6% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, H, B
- BMA · beta-D-mannopyranose · sugar · chains H, L
- MAN · alpha-D-mannopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.65 | 0.74 | 70 | empty |
| 2 | 233 | 0.64 | 0.83 | 25 | empty |
| 3 | 406 | 0.57 | 0.74 | 43 | empty |
| 4 | 116 | 0.54 | 0.82 | 20 | empty |
| 5 | 100 | 0.44 | 0.79 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3154 Ų buried · 43 hydrogen bonds · protein-protein
- H–L · 1662 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 536 Ų buried · 11 hydrogen bonds · protein-protein
- B–L · 340 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 201 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5JW3 · Structure of MEDI8852 Fab Fragment in Complex with H7 HA · 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 Q701U0
- Elsewhere: RCSB PDB 5JW3 · PDBe 5JW3 · UniProt Q701U0
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