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Structure of the A_CANINE_COLORADO_17864_06 H3 haemagglutinin in complex with 3SLN
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
- 4UO5
- Type
- protein
- Length
- 1,479 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H3 haemagglutinin HA1 chain; H3 haemagglutinin HA2 chain
- UniProt
- E0UVR5
- Ligands
- NAG, BMA, MAN, GAL, SIA, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H3 haemagglutinin HA1 chain | protein | 319 | 9% helix, 40% strand | E0UVR5 |
| B, D, F | H3 haemagglutinin HA2 chain | protein | 175 | 49% helix, 15% strand | E0UVR5 |
| C | H3 haemagglutinin HA1 chain | protein | 317 | 9% helix, 41% strand | E0UVR5 |
| E | H3 haemagglutinin HA1 chain | protein | 318 | 9% helix, 42% strand | E0UVR5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, E, B, C, D
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains E, A, C
- MAN · alpha-D-mannopyranose · sugar · 7 copies
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.87 | 0.88 | 89 | empty |
| 2 | 340 | 0.84 | 0.93 | 39 | empty |
| 3 | 221 | 0.72 | 0.88 | 30 | empty |
| 4 | 648 | 0.71 | 0.79 | 58 | empty |
| 5 | 476 | 0.71 | 0.81 | 56 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3005 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 3001 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2951 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 1683 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1656 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 4UO5 · Structure of the A_Canine_Colorado_17864_06 H3 haemagglutinin in complex with 3SLN · 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 4UO5 · PDBe 4UO5 · UniProt E0UVR5
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