Research workbench
Ebola virus gp (mucin deleted, makona strain) bound to antibody Fab ebov-296 and ebov-515
Analyse Ebola virus gp (mucin deleted, makona strain) bound to antibody Fab ebov-296… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KF9
- Type
- protein
- Length
- 1,662 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab ebov-296 heavy chain; Virion spike glycoprotein 1; Virion spike glycoprotein…
- UniProt
- A0A1C4HDV6, A0A0E3XK95
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, I, H | Antibody Fab ebov-296 heavy chain | protein | 131 | 5% helix, 47% strand | — |
| A, C, B | Virion spike glycoprotein 1 | protein | 221 | 12% helix, 41% strand | A0A1C4HDV6 |
| D, F, E | Virion spike glycoprotein 2 | protein | 92 | 48% helix, 14% strand | A0A0E3XK95 |
| J, L, K | Antibody Fab ebov-296 light chain | protein | 110 | 5% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, D, C, F, B, E, G, I, H
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, E, D, C, F, B
- BMA · beta-D-mannopyranose · sugar · 3 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.85 | 0.86 | 99 | empty |
| 2 | 142 | 0.69 | 0.89 | 31 | empty |
| 3 | 145 | 0.69 | 0.89 | 29 | empty |
| 4 | 134 | 0.67 | 0.89 | 30 | empty |
| 5 | 118 | 0.65 | 0.88 | 26 | empty |
Interfaces
24 interfaces between chains.
- B–E · 2491 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2490 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2489 Ų buried · 28 hydrogen bonds · protein-protein
- H–K · 882 Ų buried · 8 hydrogen bonds · protein-protein
- I–L · 881 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KF9 · Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515 · the same entry in another collection · chain G against G, 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 7KF9 · PDBe 7KF9 · UniProt A0A1C4HDV6 · UniProt A0A0E3XK95
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