MolNFT v1 · #159725 · protein
Ebola virus glycoprotein in complex with ebov-520 Fab
6OZ9 · Small secreted glycoprotein sgp: “Ebola virus glycoprotein in complex with ebov-520 Fab”. X-ray diffraction, 2 ligands (NAG, BMA), 11 pockets (best druggability 0.74). MolNFT v1 #159725 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6OZ9
- Type
- protein
- Length
- 708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small secreted glycoprotein sgp; Envelope glycoprotein; Ebov-520 Fab light chain…
- UniProt
- A0A0E3H7K0, A0A0E3H7K2
- Ligands
- NAG, BMA
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small secreted glycoprotein sgp | protein | 158 | 8% helix, 42% strand | A0A0E3H7K0 |
| B | Envelope glycoprotein | protein | 113 | 37% helix, 9% strand | A0A0E3H7K2 |
| L | Ebov-520 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| H | Ebov-520 Fab heavy chain | protein | 223 | 0% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.74 | 0.97 | 20 | empty |
| 2 | 560 | 0.62 | 0.74 | 60 | empty |
| 3 | 130 | 0.57 | 0.83 | 20 | empty |
| 4 | 179 | 0.56 | 0.80 | 26 | empty |
| 5 | 125 | 0.48 | 0.78 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2610 Ų buried · 29 hydrogen bonds · protein-protein
- L–H · 1900 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 461 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 452 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 260 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6OZ9 · Ebola virus glycoprotein in complex with EBOV-520 Fab · 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 A0A0E3H7K0
- Every structure of UniProt A0A0E3H7K2
- Elsewhere: RCSB PDB 6OZ9 · PDBe 6OZ9 · UniProt A0A0E3H7K0 · UniProt A0A0E3H7K2
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