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
- 2HMG
- Type
- protein
- Length
- 1,509 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin (HA1 chain); Hemagglutinin (HA2 chain)
- UniProt
- P03437
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin (HA1 chain) | protein | 328 | 9% helix, 38% strand | P03437 |
| B, D, F | Hemagglutinin (HA2 chain) | 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.88 | 0.90 | 96 | empty |
| 2 | 240 | 0.83 | 0.95 | 21 | empty |
| 3 | 96 | 0.75 | 0.96 | 24 | empty |
| 4 | 96 | 0.74 | 0.96 | 23 | empty |
| 5 | 688 | 0.74 | 0.80 | 69 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3078 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 3072 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2983 Ų buried · 48 hydrogen bonds · protein-protein
- B–F · 1545 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1526 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 2HMG · 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 2HMG · PDBe 2HMG · UniProt P03437
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