Research workbench
Refinement of the influenza virus hemagglutinin by simulated annealing
Analyse Refinement of the influenza virus hemagglutinin by simulated annealing in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HMG
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- P03437
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 328 | 9% helix, 39% strand | P03437 |
| B, D, F | Hemagglutinin | protein | 175 | 53% helix, 15% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, E, C, B, D, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.88 | 0.90 | 75 | empty |
| 2 | 247 | 0.83 | 0.95 | 23 | empty |
| 3 | 1101 | 0.76 | 0.78 | 124 | empty |
| 4 | 89 | 0.74 | 0.96 | 23 | empty |
| 5 | 453 | 0.74 | 0.83 | 61 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3120 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3083 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3058 Ų buried · 46 hydrogen bonds · protein-protein
- D–F · 1558 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 1552 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 3HMG · Refinement of the influenza virus hemagglutinin by simulated annealing · 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 P03437
- Elsewhere: RCSB PDB 3HMG · PDBe 3HMG · UniProt P03437
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