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Crystal structure of ebov glycoprotein with modified HR1C and HR2 stalk at 3.2 a resolution
Analyse Crystal structure of ebov glycoprotein with modified HR1C and HR2 stalk at 3.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JPH
- Type
- protein
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- NAG, MAN, BMA, PO4
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein | protein | 262 | 11% helix, 33% strand | — |
| B | Envelope glycoprotein | protein | 136 | 39% helix, 11% strand | Q05320 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.61 | 0.83 | 26 | empty |
| 2 | 249 | 0.54 | 0.77 | 31 | empty |
| 3 | 112 | 0.51 | 0.81 | 19 | PO4 |
| 4 | 123 | 0.45 | 0.77 | 20 | empty |
| 5 | 116 | 0.40 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2909 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7JPH · Crystal structure of EBOV glycoprotein with modified HR1c and HR2 stalk at 3.2 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 Q05320
- Elsewhere: RCSB PDB 7JPH · PDBe 7JPH · UniProt Q05320
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