Research workbench
Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form
Analyse Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QQB
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C7S226
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 324 | 10% helix, 40% strand | C7S226 |
| B | Hemagglutinin | protein | 172 | 57% helix, 13% strand | C7S226 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.63 | 0.79 | 44 | empty |
| 2 | 56 | 0.37 | 0.80 | 12 | empty |
| 3 | 67 | 0.33 | 0.76 | 16 | empty |
| 4 | 81 | 0.32 | 0.74 | 19 | empty |
| 5 | 50 | 0.27 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2588 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3QQB · Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form · 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 C7S226
- Elsewhere: RCSB PDB 3QQB · PDBe 3QQB · UniProt C7S226
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