MolNFT v1 · #98557 · protein
The structure of hemagglutinin from avian-origin H7N9 influenza virus (A/SHANGHAI/1/2013)
4LCX · Hemagglutinin HA1: “The structure of hemagglutinin from avian-origin H7N9 influenza virus (A/SHANGHAI/1/2013)”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #98557 on GenesisL1: 3D structure…
- PDB
- 4LCX
- Type
- protein
- Length
- 1,458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 316 | 9% helix, 36% strand | — |
| B, D, F | Hemagglutinin HA2 | protein | 170 | 56% helix, 12% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.83 | 0.97 | 19 | empty |
| 2 | 714 | 0.83 | 0.86 | 52 | empty |
| 3 | 164 | 0.81 | 0.97 | 27 | empty |
| 4 | 929 | 0.81 | 0.83 | 120 | empty |
| 5 | 163 | 0.81 | 0.96 | 27 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3127 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 3124 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3121 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1496 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1450 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4LCX · The structure of hemagglutinin from avian-origin H7N9 influenza virus (A/Shanghai/1/2013) · 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
- Elsewhere: RCSB PDB 4LCX · PDBe 4LCX
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