Research workbench
Crystal structure of HPIV3 hemagglutinin-neuraminidase, H552Q/Q559R mutant
Analyse Crystal structure of HPIV3 hemagglutinin-neuraminidase, H552Q/Q559R mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MZE
- Type
- protein
- Length
- 864 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-neuraminidase
- EC
- 3.2.1.18
- UniProt
- P08492
- Ligands
- NAG, MAN, BMA, FUL, CA, PO4, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin-neuraminidase (EC 3.2.1.18) | protein | 432 | 5% helix, 45% strand | P08492 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.80 | 0.90 | 44 | PO4 |
| 2 | 428 | 0.69 | 0.80 | 36 | PO4, EDO, PEG, SO4 |
| 3 | 401 | 0.66 | 0.79 | 37 | PO4, EDO, PEG |
| 4 | 190 | 0.64 | 0.84 | 31 | empty |
| 5 | 163 | 0.59 | 0.82 | 27 | EDO |
Interfaces
1 interface between chains.
- A–B · 1453 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4MZE · Crystal structure of hPIV3 hemagglutinin-neuraminidase, H552Q/Q559R mutant · 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 P08492
- Elsewhere: RCSB PDB 4MZE · PDBe 4MZE · UniProt P08492
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