Research workbench
Crystal structure of influenza a virus H5 hemagglutinin globular head in complex with the Fab of antibody 3C11
Analyse Crystal structure of influenza a virus H5 hemagglutinin globular head in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IUV
- Type
- protein
- Length
- 1,307 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; 3C11 light chain; 3C11 heavy chain
- UniProt
- Q77XR4
- Ligands
- NAG, FUC
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 213 | 12% helix, 40% strand | Q77XR4 |
| L, D | 3C11 light chain | protein | 215 | 6% helix, 52% strand | — |
| H | 3C11 heavy chain | protein | 228 | 6% helix, 53% strand | — |
| B | Hemagglutinin | protein | 212 | 13% helix, 41% strand | Q77XR4 |
| C | 3C11 heavy chain | protein | 224 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, H, B, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, L, H, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.73 | 0.76 | 96 | empty |
| 2 | 579 | 0.71 | 0.80 | 55 | empty |
| 3 | 349 | 0.71 | 0.83 | 41 | empty |
| 4 | 377 | 0.70 | 0.82 | 42 | empty |
| 5 | 558 | 0.70 | 0.79 | 54 | empty |
Interfaces
9 interfaces between chains.
- D–C · 1853 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 1832 Ų buried · 20 hydrogen bonds · protein-protein
- L–B · 720 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 700 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 625 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6IUV · Crystal structure of influenza A virus H5 hemagglutinin globular head in complex with the… · 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 Q77XR4
- Elsewhere: RCSB PDB 6IUV · PDBe 6IUV · UniProt Q77XR4
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