Research workbench
Crystal structure of Fab 8M2 in complex with a H2N2 influenza virus hemagglutinin
Analyse Crystal structure of Fab 8M2 in complex with a H2N2 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HFU
- Type
- protein
- Length
- 929 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Fab 8M2 heavy chain; Fab 8M2 light chain
- UniProt
- Q67085
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 320 | 8% helix, 39% strand | Q67085 |
| B | Hemagglutinin HA2 | protein | 172 | 55% helix, 13% strand | Q67085 |
| H | Fab 8M2 heavy chain | protein | 224 | 5% helix, 50% strand | — |
| L | Fab 8M2 light chain | protein | 213 | 4% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
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 | 54 | 0.65 | 0.95 | 21 | empty |
| 2 | 250 | 0.62 | 0.81 | 23 | empty |
| 3 | 269 | 0.58 | 0.78 | 40 | empty |
| 4 | 366 | 0.55 | 0.74 | 46 | empty |
| 5 | 148 | 0.41 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2746 Ų buried · 40 hydrogen bonds · protein-protein
- H–L · 1923 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 828 Ų buried · 10 hydrogen bonds · protein-protein
- A–L · 182 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4HFU · Crystal structure of Fab 8M2 in complex with a H2N2 influenza virus hemagglutinin · 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 Q67085
- Elsewhere: RCSB PDB 4HFU · PDBe 4HFU · UniProt Q67085
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