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Structure of the A_EQUINE_RICHMOND_07 H3 haemagglutinin in complex with sialyl lewis X
Analyse Structure of the A_EQUINE_RICHMOND_07 H3 haemagglutinin in complex with sialyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UO2
- Type
- protein
- Length
- 1,485 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
- C3TUR9
- Ligands
- NAG, BMA, MAN, FUC, GAL, SIA
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H3 haemagglutinin HA1 chain | protein | 325 | 10% helix, 41% strand | C3TUR9 |
| B, F | H3 haemagglutinin HA2 chain | protein | 172 | 52% helix, 16% strand | C3TUR9 |
| C | H3 haemagglutinin HA1 chain | protein | 320 | 10% helix, 39% strand | C3TUR9 |
| D | H3 haemagglutinin HA2 chain | protein | 171 | 50% helix, 16% strand | C3TUR9 |
| E | H3 haemagglutinin HA1 chain | protein | 325 | 10% helix, 38% strand | C3TUR9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 44 copies · chains A, E, B, C, D, F
- BMA · beta-D-mannopyranose · sugar · 10 copies · chains E, A, C
- MAN · alpha-D-mannopyranose · sugar · 7 copies
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains A, B, C, D, E, F
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.86 | 0.87 | 146 | empty |
| 2 | 288 | 0.85 | 0.95 | 35 | empty |
| 3 | 1084 | 0.79 | 0.80 | 111 | empty |
| 4 | 512 | 0.75 | 0.83 | 69 | empty |
| 5 | 444 | 0.71 | 0.82 | 54 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3107 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 3033 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3029 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 1515 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1472 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 glycan, 15 disulfide (N-glycosylation, disulfide).
Compared structures
- 4UO2 · Structure of the A_Equine_Richmond_07 H3 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 C3TUR9
- Elsewhere: RCSB PDB 4UO2 · PDBe 4UO2 · UniProt C3TUR9
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