MolNFT v1 · #66821 · protein
Structure of bovine torovirus hemagglutinin-esterase
3I26: “Structure of bovine torovirus hemagglutinin-esterase”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 7 pockets (best druggability 0.80). MolNFT v1 #66821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3I26
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- EC
- 3.1.1.53
- UniProt
- P0C0V9
- Ligands
- NAG, MAN, BMA
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 365 | 16% helix, 35% strand | P0C0V9 |
| B | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 364 | 16% helix, 34% strand | P0C0V9 |
| C | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 358 | 16% helix, 35% strand | P0C0V9 |
| D | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 369 | 16% helix, 34% strand | P0C0V9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, D, B, C
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains D, A
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.80 | 0.82 | 136 | empty |
| 2 | 1000 | 0.75 | 0.78 | 74 | NAG |
| 3 | 451 | 0.75 | 0.83 | 61 | empty |
| 4 | 353 | 0.65 | 0.80 | 57 | empty |
| 5 | 88 | 0.48 | 0.82 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1097 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1048 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 350 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 3I26 · Structure of bovine torovirus Hemagglutinin-Esterase · 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 P0C0V9
- Elsewhere: RCSB PDB 3I26 · PDBe 3I26 · UniProt P0C0V9
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