Research workbench
Structure of the A_MALLARD_SWEDEN_51_2002 H10 avian haemmaglutinin in complex with avian receptor analog lsta
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
- 4CYZ
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- E0YNJ7
- Ligands
- NAG, MAN, BMA, GAL, SIA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 318 | 9% helix, 42% strand | E0YNJ7 |
| B, D, F | Hemagglutinin | protein | 172 | 55% helix, 14% strand | E0YNJ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, C, D, A, E, F
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, E
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.86 | 0.88 | 129 | empty |
| 2 | 183 | 0.83 | 0.97 | 23 | empty |
| 3 | 159 | 0.80 | 0.96 | 38 | EDO |
| 4 | 90 | 0.76 | 0.97 | 18 | EDO |
| 5 | 322 | 0.75 | 0.86 | 45 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3161 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3149 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 3118 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 1550 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1546 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4CYZ · Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with avian… · 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 E0YNJ7
- Elsewhere: RCSB PDB 4CYZ · PDBe 4CYZ · UniProt E0YNJ7
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