Research workbench
Crystal structure of H12 haemagglutinin
Analyse Crystal structure of H12 haemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A9D
- Type
- protein
- Length
- 966 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C6KJK3, P03446
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemagglutinin | protein | 322 | 8% helix, 39% strand | C6KJK3 |
| B | Hemagglutinin | protein | 155 | 52% helix, 10% strand | P03446 |
| D | Hemagglutinin | protein | 167 | 53% helix, 14% strand | P03446 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.58 | 0.76 | 32 | empty |
| 2 | 135 | 0.58 | 0.83 | 20 | empty |
| 3 | 130 | 0.57 | 0.83 | 16 | empty |
| 4 | 451 | 0.56 | 0.73 | 44 | empty |
| 5 | 113 | 0.50 | 0.81 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2818 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2770 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7A9D · Crystal structure of H12 Haemagglutinin · 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 C6KJK3
- Every structure of UniProt P03446
- Elsewhere: RCSB PDB 7A9D · PDBe 7A9D · UniProt C6KJK3 · UniProt P03446
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