MolNFT v1 · #24358 · protein
Newcastle disease virus hemagglutinin-neuraminidase: evidence for a second sialic acid binding site and implications for fusion
1USR · Hemagglutinin-neuraminidase glycoprotein: “Newcastle disease virus hemagglutinin-neuraminidase: evidence for a second sialic acid binding site and…”. X-ray diffraction, 5 ligands (DAN, WIA, SIA), 7 pockets (best druggability 0.73).…
- PDB
- 1USR
- Type
- protein
- Length
- 893 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase glycoprotein
- EC
- 3.2.1.18
- UniProt
- P32884
- Ligands
- DAN, WIA, SIA, NDG, CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin-neuraminidase glycoprotein (EC 3.2.1.18) | protein | 447 | 8% helix, 44% strand | P32884 |
| B | Hemagglutinin-neuraminidase glycoprotein (EC 3.2.1.18) | protein | 446 | 8% helix, 44% strand | P32884 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- WIA · methyl 6-thio-beta-D-galactopyranoside · ligand · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, 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 | 59 | 0.73 | 0.99 | 20 | empty |
| 2 | 333 | 0.67 | 0.81 | 33 | DAN |
| 3 | 339 | 0.67 | 0.81 | 35 | DAN |
| 4 | 105 | 0.51 | 0.82 | 20 | empty |
| 5 | 105 | 0.48 | 0.80 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1853 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 1USR · Newcastle disease virus hemagglutinin-neuraminidase: Evidence for a second sialic acid… · 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 1USR · PDBe 1USR · UniProt P32884
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