Research workbench
Crystal structure of nipah virus fusion glycoprotein in the prefusion state
Analyse Crystal structure of nipah virus fusion glycoprotein in the prefusion state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EVM
- Type
- protein
- Length
- 2,724 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- UniProt
- Q9IH63
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Fusion glycoprotein F0 | protein | 456 | 35% helix, 26% strand | Q9IH63 |
| C, F | Fusion glycoprotein F0 | protein | 450 | 36% helix, 28% strand | Q9IH63 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 23 copies · chains C
- BMA · beta-D-mannopyranose · sugar
- MLI · Malonate ion · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.81 | 0.82 | 63 | MLI |
| 2 | 1104 | 0.81 | 0.82 | 63 | MLI |
| 3 | 976 | 0.77 | 0.79 | 82 | empty |
| 4 | 500 | 0.65 | 0.77 | 67 | empty |
| 5 | 351 | 0.62 | 0.78 | 46 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3087 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 3016 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 2988 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2985 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2963 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 5EVM · Crystal Structure of Nipah Virus Fusion Glycoprotein in the Prefusion State · 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 Q9IH63
- Elsewhere: RCSB PDB 5EVM · PDBe 5EVM · UniProt Q9IH63
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