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Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/DUCK/EGYPT/10185SS/2010 (H5N1) with lsta
Analyse Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E2Z
- Type
- protein
- Length
- 1,494 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- G8IPF0
- Ligands
- NAG, FUL, GAL, SIA, FUC
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, E | Hemagglutinin | protein | 323 | 10% helix, 41% strand | G8IPF0 |
| D, B, F | Hemagglutinin | protein | 175 | 54% helix, 11% strand | G8IPF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains C, A, E
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains C, A, E
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains C, A, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains C, A, E
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.84 | 0.90 | 74 | empty |
| 2 | 984 | 0.84 | 0.85 | 100 | empty |
| 3 | 100 | 0.78 | 0.98 | 15 | empty |
| 4 | 496 | 0.66 | 0.78 | 55 | empty |
| 5 | 366 | 0.64 | 0.79 | 44 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2591 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2510 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2481 Ų buried · 32 hydrogen bonds · protein-protein
- B–F · 1373 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1319 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5E2Z · Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus… · the same entry in another collection · chain D against D, 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 G8IPF0
- Elsewhere: RCSB PDB 5E2Z · PDBe 5E2Z · UniProt G8IPF0
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