Research workbench
Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/DUCK/EGYPT/10185SS/2010 (H5N1) with lstc
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
- 5E30
- 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, GAL, FUL, SIA, FUC
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% 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, 12% strand | G8IPF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains C, A, E
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains C, A, E
- FUL · beta-L-fucopyranose · 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.86 | 0.87 | 114 | empty |
| 2 | 78 | 0.77 | 0.99 | 15 | empty |
| 3 | 1001 | 0.72 | 0.76 | 122 | empty |
| 4 | 410 | 0.65 | 0.79 | 46 | empty |
| 5 | 398 | 0.65 | 0.79 | 56 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2610 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2535 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2521 Ų buried · 39 hydrogen bonds · protein-protein
- B–F · 1537 Ų buried · 18 hydrogen bonds · protein-protein
- D–B · 1493 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5E30 · 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 5E30 · PDBe 5E30 · UniProt G8IPF0
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