Research workbench
Ebola virus gp (mucin deleted, makona strain) bound to antibody Fab ebov-293
Analyse Ebola virus gp (mucin deleted, makona strain) bound to antibody Fab ebov-293 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KEX
- Type
- protein
- Length
- 1,620 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab ebov-293 light chain; Antibody Fab ebov-293 heavy chain; Virion spike…
- UniProt
- A0A1C4HDV6, A0A0E3XK95
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| J, K, L | Antibody Fab ebov-293 light chain | protein | 107 | 6% helix, 50% strand | — |
| G, H, I | Antibody Fab ebov-293 heavy chain | protein | 121 | 10% helix, 55% strand | — |
| A, B, C | Virion spike glycoprotein 1 | protein | 220 | 12% helix, 36% strand | A0A1C4HDV6 |
| D, E, F | Virion spike glycoprotein 2 | protein | 92 | 49% helix, 17% strand | A0A0E3XK95 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, D, E, B, F, C
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.87 | 0.89 | 107 | empty |
| 2 | 107 | 0.69 | 0.91 | 22 | empty |
| 3 | 101 | 0.68 | 0.91 | 29 | empty |
| 4 | 92 | 0.67 | 0.92 | 25 | empty |
| 5 | 110 | 0.66 | 0.89 | 31 | empty |
Interfaces
24 interfaces between chains.
- A–D · 2393 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2391 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 2391 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 750 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 749 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7KEX · Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-293 · the same entry in another collection · chain J against J, 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 A0A1C4HDV6
- Every structure of UniProt A0A0E3XK95
- Elsewhere: RCSB PDB 7KEX · PDBe 7KEX · UniProt A0A1C4HDV6 · UniProt A0A0E3XK95
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