Research workbench
Structural basis of ebola virus entry: viral glycoprotein bound to its endosomal receptor niemann-pick C1
Analyse Structural basis of ebola virus entry: viral glycoprotein bound to its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F1B
- Type
- protein
- Length
- 460 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP1; GP2; Niemann-pick C1 protein
- UniProt
- P87666, O15118
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GP1 | protein | 158 | 6% helix, 42% strand | P87666 |
| B | GP2 | protein | 87 | 45% helix, 16% strand | P87666 |
| C | Niemann-pick C1 protein | protein | 215 | 34% helix, 20% strand | O15118 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.55 | 0.79 | 23 | empty |
| 2 | 165 | 0.51 | 0.78 | 29 | empty |
| 3 | 85 | 0.39 | 0.77 | 12 | empty |
| 4 | 70 | 0.36 | 0.77 | 14 | empty |
| 5 | 94 | 0.33 | 0.73 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2225 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 710 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5F1B · Structural basis of Ebola virus entry: viral glycoprotein bound to its endosomal receptor… · the same entry in another collection · chain A against A, TM-score 1.00
- O15118 · AlphaFold monomer V2.0 prediction for npc intracellular cholesterol transporter 1 (O15118) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P87666
- Every structure of UniProt O15118
- Elsewhere: RCSB PDB 5F1B · PDBe 5F1B · UniProt P87666 · UniProt O15118
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