Research workbench
Crystal structure of mouse hepatitis virus strain dvim hemagglutinin- esterase
Analyse Crystal structure of mouse hepatitis virus strain dvim hemagglutinin- esterase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JIF
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- EC
- 3.1.1.53
- UniProt
- O92367
- Ligands
- NAG, MAN, BMA, NA
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 363 | 16% helix, 32% strand | O92367 |
| B | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 355 | 15% helix, 33% strand | O92367 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.65 | 0.74 | 71 | empty |
| 2 | 102 | 0.60 | 0.86 | 21 | GOL |
| 3 | 128 | 0.48 | 0.78 | 28 | empty |
| 4 | 123 | 0.47 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1291 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 5JIF · Crystal structure of mouse hepatitis virus strain DVIM 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 O92367
- Elsewhere: RCSB PDB 5JIF · PDBe 5JIF · UniProt O92367
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