Research workbench
X-31 hemagglutinin precursor HA0 at pH 7.5 after reneutralization
Analyse X-31 hemagglutinin precursor HA0 at pH 7.5 after reneutralization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZJ8
- Type
- protein
- Length
- 1,482 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HEMAGGLUTININ,FIBRITIN
- UniProt
- P03437
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 16 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | HEMAGGLUTININ,FIBRITIN | protein | 494 | 24% helix, 30% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains C, A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.86 | 0.88 | 113 | BOG |
| 2 | 923 | 0.82 | 0.84 | 81 | empty |
| 3 | 887 | 0.75 | 0.79 | 84 | empty |
| 4 | 855 | 0.74 | 0.79 | 75 | empty |
| 5 | 57 | 0.72 | 0.98 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2112 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 2108 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2104 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZJ8 · X-31 Hemagglutinin Precursor HA0 at pH 7.5 after reneutralization · 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 7ZJ8 · PDBe 7ZJ8 · UniProt P03437
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