Research workbench
Structure of ebov gp lacking the mucin-like domain with 1C11 scfv and 1C3 Fab bound
Analyse Structure of ebov gp lacking the mucin-like domain with 1C11 scfv and 1C3 Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SWD
- Type
- protein
- Length
- 1,652 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion spike glycoprotein GP1; Virion spike glycoprotein GP2; 1C11 scfv; 1C3 heavy chain…
- UniProt
- A0A089X075, A0A7S6GAH2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 7 distinct chains · 8% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Virion spike glycoprotein GP1 | protein | 151 | 7% helix, 38% strand | A0A089X075 |
| B, D, F | Virion spike glycoprotein GP2 | protein | 96 | 47% helix, 10% strand | A0A7S6GAH2 |
| E | Virion spike glycoprotein GP1 | protein | 147 | 10% helix, 32% strand | A0A089X075 |
| G, H | 1C11 scfv | protein | 226 | 1% helix, 46% strand | — |
| I | 1C11 scfv | protein | 229 | 3% helix, 44% strand | — |
| J | 1C3 heavy chain | protein | 121 | 2% helix, 40% strand | — |
| K | 1C3 light chain | protein | 113 | 0% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, D, I, E, F, H, A, B, G
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains I, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.86 | 0.89 | 97 | empty |
| 2 | 235 | 0.74 | 0.89 | 42 | empty |
| 3 | 54 | 0.70 | 0.98 | 20 | empty |
| 4 | 53 | 0.69 | 0.98 | 20 | empty |
| 5 | 130 | 0.66 | 0.89 | 30 | empty |
Interfaces
30 interfaces between chains.
- A–B · 2422 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2408 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2402 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 919 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 826 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7SWD · Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound · 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 A0A089X075
- Every structure of UniProt A0A7S6GAH2
- Elsewhere: RCSB PDB 7SWD · PDBe 7SWD · UniProt A0A089X075 · UniProt A0A7S6GAH2
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