Research workbench
Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin in complex with avian receptor analog su-3SLN
Analyse Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CZ0
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin
- UniProt
- E0YNJ7
- Ligands
- NGS, NAG, MAN, GAL, SIA, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Haemagglutinin | protein | 318 | 8% helix, 42% strand | E0YNJ7 |
| B, D, F | Haemagglutinin | protein | 172 | 55% helix, 9% strand | E0YNJ7 |
Ligands and binding sites
- NGS · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose · ligand · 3 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains C, A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, E, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, E, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.85 | 0.92 | 40 | empty |
| 2 | 192 | 0.84 | 0.97 | 24 | empty |
| 3 | 151 | 0.80 | 0.97 | 34 | empty |
| 4 | 118 | 0.77 | 0.96 | 30 | empty |
| 5 | 231 | 0.76 | 0.90 | 31 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3198 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3195 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 3162 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 1542 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1491 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4CZ0 · Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with avian… · the same entry in another collection · chain B against B, 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 E0YNJ7
- Elsewhere: RCSB PDB 4CZ0 · PDBe 4CZ0 · UniProt E0YNJ7
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