Research workbench
Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133A deletion) from the influenza virus A/CHICKEN/VIETNAM/NCVD- 093/2008 (H5N1) with lstc
Analyse Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E35
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C4P282
- Ligands
- NAG, GAL, SIA
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 323 | 10% helix, 40% strand | C4P282 |
| B | Hemagglutinin | protein | 170 | 58% helix, 10% strand | C4P282 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.64 | 0.80 | 42 | empty |
| 2 | 84 | 0.30 | 0.72 | 18 | empty |
| 3 | 64 | 0.29 | 0.73 | 12 | empty |
| 4 | 51 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2450 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5E35 · Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133a deletion)… · 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 C4P282
- Elsewhere: RCSB PDB 5E35 · PDBe 5E35 · UniProt C4P282
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