MolNFT v1 · #116986 · protein
Crystal structure of influenza a virus H5 hemagglutinin globular head in complex with the Fab of antibody 65C6
5DUM · 65C6 heavy chain: “Crystal structure of influenza a virus H5 hemagglutinin globular head in complex with the Fab of antibody 65C6”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.72). MolNFT v1 #116986 on…
- PDB
- 5DUM
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 65C6 heavy chain; 65C6 light chain; Hemagglutinin
- UniProt
- Q1WDM0
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 65C6 heavy chain | protein | 219 | 5% helix, 51% strand | — |
| L | 65C6 light chain | protein | 211 | 4% helix, 53% strand | — |
| A | Hemagglutinin | protein | 197 | 12% helix, 37% strand | Q1WDM0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.72 | 0.90 | 33 | empty |
| 2 | 113 | 0.49 | 0.80 | 13 | empty |
| 3 | 229 | 0.48 | 0.74 | 33 | empty |
| 4 | 54 | 0.32 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1849 Ų buried · 19 hydrogen bonds · protein-protein
- H–A · 683 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 65 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5DUM · Crystal structure of influenza A virus H5 hemagglutinin globular head in complex with the… · the same entry in another collection · chain H against H, 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 Q1WDM0
- Elsewhere: RCSB PDB 5DUM · PDBe 5DUM · UniProt Q1WDM0
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