Research workbench
Structure of porcine torovirus hemagglutinin-esterase in complex with its receptor
Analyse Structure of porcine torovirus hemagglutinin-esterase in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I1L
- Type
- protein
- Length
- 1,086 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase protein
- EC
- 3.1.1.53
- UniProt
- Q70KP4
- Ligands
- SIO, NAG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin-esterase protein (EC 3.1.1.53) | protein | 362 | 17% helix, 33% strand | Q70KP4 |
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 · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C
- ACY · Acetic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.72 | 0.77 | 96 | SIO, ACY, NAG |
| 2 | 69 | 0.72 | 0.97 | 21 | empty |
| 3 | 807 | 0.70 | 0.76 | 77 | empty |
| 4 | 94 | 0.34 | 0.73 | 15 | empty |
| 5 | 62 | 0.31 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1413 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 264 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 3I1L · Structure of porcine torovirus Hemagglutinin-Esterase in complex with its receptor · 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 Q70KP4
- Elsewhere: RCSB PDB 3I1L · PDBe 3I1L · UniProt Q70KP4
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