MolNFT v1 · #84529 · protein
H5 haemagglutinin in complex with sialyl-lewis X
3ZNM: “H5 haemagglutinin in complex with sialyl-lewis X”. X-ray diffraction, 4 ligands (NAG, GLA, SIA), 18 pockets (best druggability 0.88). MolNFT v1 #84529 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZNM
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin
- UniProt
- Q6DQ34
- Ligands
- NAG, GLA, SIA, FUC
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Haemagglutinin | protein | 321 | 9% helix, 37% strand | Q6DQ34 |
| B, D, F | Haemagglutinin | protein | 163 | 56% helix, 13% strand | Q6DQ34 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- GLA · alpha-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, C, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.88 | 0.89 | 133 | empty |
| 2 | 54 | 0.72 | 0.99 | 15 | empty |
| 3 | 760 | 0.72 | 0.78 | 94 | empty |
| 4 | 60 | 0.71 | 0.98 | 12 | empty |
| 5 | 344 | 0.65 | 0.80 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2452 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2444 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2443 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1328 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1327 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 3ZNM · H5 Haemagglutinin in Complex with Sialyl-Lewis X · 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 Q6DQ34
- Elsewhere: RCSB PDB 3ZNM · PDBe 3ZNM · UniProt Q6DQ34
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