MolNFT v1 · #117809 · protein
Crystal structure of prefusion hendra virus F protein
5EJB · Fusion glycoprotein F0: “Crystal structure of prefusion hendra virus F protein”. X-ray diffraction, 2 ligands (NAG, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #117809 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5EJB
- Type
- protein
- Length
- 2,673 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0
- Ligands
- NAG, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Fusion glycoprotein F0 | protein | 447 | 34% helix, 29% strand | — |
| C | Fusion glycoprotein F0 | protein | 454 | 33% helix, 27% strand | — |
| D | Fusion glycoprotein F0 | protein | 460 | 34% helix, 28% strand | — |
| F, E | Fusion glycoprotein F0 | protein | 436 | 34% helix, 29% strand | — |
| A | Fusion glycoprotein F0 | protein | 440 | 33% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains B, C, D, E, F, A
- SO4 · Sulfate ion · ion · 6 copies · chains B, C, A, 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 | 1036 | 0.81 | 0.82 | 61 | empty |
| 2 | 1049 | 0.81 | 0.82 | 62 | empty |
| 3 | 968 | 0.75 | 0.78 | 89 | empty |
| 4 | 614 | 0.68 | 0.77 | 68 | empty |
| 5 | 539 | 0.66 | 0.77 | 70 | empty |
Interfaces
9 interfaces between chains.
- C–A · 2894 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 2863 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 2853 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2825 Ų buried · 25 hydrogen bonds · protein-protein
- F–E · 2821 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5EJB · Crystal structure of prefusion Hendra virus F protein · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 5EJB · PDBe 5EJB
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