MolNFT v1 · #87661 · protein
Crystal structure of mouse hepatitis virus strain S hemagglutinin- esterase in complex with 4-O-acetylated sialic acid
4C7W · Hemagglutinin-esterase: “Crystal structure of mouse hepatitis virus strain S hemagglutinin- esterase in complex with 4-O-acetylated…”. X-ray diffraction, 5 ligands (SIO, NAG, BMA), 6 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 4C7W
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- EC
- 3.1.1.53
- UniProt
- O55252
- Ligands
- SIO, NAG, BMA, MAN, K
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 353 | 11% helix, 33% strand | O55252 |
| B | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 334 | 12% helix, 34% strand | O55252 |
Ligands and binding sites
- SIO · methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.67 | 0.74 | 52 | empty |
| 2 | 245 | 0.56 | 0.78 | 25 | empty |
| 3 | 158 | 0.48 | 0.77 | 26 | empty |
| 4 | 67 | 0.34 | 0.77 | 19 | empty |
| 5 | 54 | 0.32 | 0.76 | 18 | SIO |
Interfaces
1 interface between chains.
- A–B · 1600 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4C7W · Crystal structure of Mouse Hepatitis virus strain S Hemagglutinin- esterase in complex… · 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 O55252
- Elsewhere: RCSB PDB 4C7W · PDBe 4C7W · UniProt O55252
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