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Structure of the A_CANINE_COLORADO_17864_06 H3 haemagglutinin in complex with 6SO4 sialyl lewis X
Analyse Structure of the A_CANINE_COLORADO_17864_06 H3 haemagglutinin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UO7
- Type
- protein
- Length
- 1,480 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin HA1; Haemagglutinin HA2
- UniProt
- E0UVR5
- Ligands
- NGS, NAG, MAN, BMA, GAL, SIA, FUC, SO4
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Haemagglutinin HA1 | protein | 319 | 9% helix, 40% strand | E0UVR5 |
| B, F | Haemagglutinin HA2 | protein | 174 | 47% helix, 13% strand | E0UVR5 |
| D | Haemagglutinin HA2 | protein | 175 | 45% helix, 13% strand | E0UVR5 |
Ligands and binding sites
- NGS · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose · ligand · 3 copies · chains A, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, E, C, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, C
- GAL · beta-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
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.86 | 0.87 | 82 | empty |
| 2 | 617 | 0.84 | 0.89 | 66 | SO4 |
| 3 | 1144 | 0.75 | 0.78 | 110 | empty |
| 4 | 632 | 0.74 | 0.80 | 81 | empty |
| 5 | 717 | 0.73 | 0.79 | 62 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2982 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2947 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2921 Ų buried · 40 hydrogen bonds · protein-protein
- B–F · 1647 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1600 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4UO7 · Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin in complex with 6SO4 Sialyl… · 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 E0UVR5
- Elsewhere: RCSB PDB 4UO7 · PDBe 4UO7 · UniProt E0UVR5
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