MolNFT v1 · #141193 · protein
Crystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor peptide (fip)
5YZD · Glycoprotein F2: “Crystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor…”. X-ray diffraction, 2 ligands (PHQ, NAG), 6 pockets (best druggability 0.46). MolNFT v1 #141193 on…
- PDB
- 5YZD
- Type
- protein
- Length
- 451 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein F2; Glycoprotein F1,MEASLES virus fusion protein; Peptide cbz-dpn-phe-gly
- UniProt
- Q786F3
- Ligands
- PHQ, NAG
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein F2 | protein | 81 | 46% helix, 32% strand | Q786F3 |
| C | Glycoprotein F1,MEASLES virus fusion protein | protein | 367 | 32% helix, 28% strand | Q786F3 |
| B | Peptide cbz-dpn-phe-gly | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
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 | 77 | 0.46 | 0.82 | 19 | empty |
| 2 | 73 | 0.38 | 0.78 | 17 | empty |
| 3 | 76 | 0.36 | 0.76 | 16 | empty |
| 4 | 67 | 0.34 | 0.76 | 21 | empty |
| 5 | 65 | 0.33 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–C · 4477 Ų buried · 68 hydrogen bonds · protein-protein
- C–B · 255 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan, 1 covalent, 1 d-amino (disulfide, N-glycosylation, covalent ligand, D-amino acid).
Compared structures
- 5YZD · Crystal structure of the prefusion form of measles virus fusion protein in complex with a… · 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 5YZD · PDBe 5YZD · UniProt Q786F3
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