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Crystal structure of the newcastle disease virus hemagglutinin- neuraminidase complexed with thiosialoside
Analyse Crystal structure of the newcastle disease virus hemagglutinin- neuraminidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1USX
- Type
- protein
- Length
- 1,338 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase glycoprotein
- EC
- 3.2.1.18
- UniProt
- P32884
- Ligands
- WIA, DAN, SIA
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin-neuraminidase glycoprotein (EC 3.2.1.18) | protein | 446 | 7% helix, 42% strand | P32884 |
Ligands and binding sites
- WIA · methyl 6-thio-beta-D-galactopyranoside · ligand · 3 copies · chains A, C
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 3 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.74 | 0.99 | 20 | empty |
| 2 | 383 | 0.69 | 0.81 | 36 | DAN |
| 3 | 370 | 0.68 | 0.81 | 38 | DAN |
| 4 | 334 | 0.67 | 0.81 | 34 | DAN |
| 5 | 384 | 0.57 | 0.75 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1811 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1USX · Crystal structure of the Newcastle disease virus hemagglutinin-neuraminidase complexed… · 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 P32884
- Elsewhere: RCSB PDB 1USX · PDBe 1USX · UniProt P32884
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