MolNFT v1 · #141151 · protein
Crystal structure of the prefusion form of measles virus fusion protein
5YXW · Glycoprotein F2: “Crystal structure of the prefusion form of measles virus fusion protein”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.42). MolNFT v1 #141151 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YXW
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein F2; Glycoprotein F1,MEASLES virus fusion protein
- UniProt
- Q786F3
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein F2 | protein | 85 | 44% helix, 31% strand | Q786F3 |
| B | Glycoprotein F1,MEASLES virus fusion protein | protein | 367 | 33% helix, 28% strand | Q786F3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.42 | 0.79 | 18 | empty |
| 2 | 75 | 0.41 | 0.79 | 17 | empty |
| 3 | 50 | 0.41 | 0.82 | 18 | empty |
| 4 | 91 | 0.37 | 0.76 | 19 | empty |
| 5 | 67 | 0.33 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4641 Ų buried · 62 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5YXW · Crystal structure of the prefusion form of measles virus fusion protein · 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 Q786F3
- Elsewhere: RCSB PDB 5YXW · PDBe 5YXW · UniProt Q786F3
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