Research workbench
Ebola virus gp (mucin deleted, makona strain) bound to antibody Fab ebov-442
Analyse Ebola virus gp (mucin deleted, makona strain) bound to antibody Fab ebov-442 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KFB
- Type
- protein
- Length
- 1,665 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion spike glycoprotein 1; Antibody Fab ebov-442 heavy chain; Antibody Fab ebov-442…
- UniProt
- A0A1C4HDV6, A0A0E3XK95
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Virion spike glycoprotein 1 | protein | 222 | 12% helix, 41% strand | A0A1C4HDV6 |
| G, H, I | Antibody Fab ebov-442 heavy chain | protein | 136 | 4% helix, 48% strand | — |
| J, K, L | Antibody Fab ebov-442 light chain | protein | 107 | 6% helix, 48% strand | — |
| D, E, F | Virion spike glycoprotein 2 | protein | 90 | 46% helix, 13% strand | A0A0E3XK95 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, D, B, E, C, F, G, J, H, K, I, L
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, F, D, B, E, C
- BMA · beta-D-mannopyranose · sugar · 6 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.86 | 0.88 | 95 | empty |
| 2 | 141 | 0.71 | 0.90 | 32 | empty |
| 3 | 164 | 0.70 | 0.89 | 36 | empty |
| 4 | 180 | 0.69 | 0.88 | 37 | empty |
| 5 | 153 | 0.66 | 0.87 | 28 | empty |
Interfaces
24 interfaces between chains.
- A–D · 2449 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 2448 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 2446 Ų buried · 29 hydrogen bonds · protein-protein
- B–H · 925 Ų buried · 14 hydrogen bonds · protein-protein
- C–I · 925 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 7KFB · Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-442 · 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 A0A1C4HDV6
- Every structure of UniProt A0A0E3XK95
- Elsewhere: RCSB PDB 7KFB · PDBe 7KFB · UniProt A0A1C4HDV6 · UniProt A0A0E3XK95
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