Research workbench
Ebov gp in complex with variable Fab domains of iggs C2G4 and C13C6
Analyse Ebov gp in complex with variable Fab domains of iggs C2G4 and C13C6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KEL
- Type
- protein
- Length
- 2,409 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ebola surface glycoprotein, GP1; Ebola surface glycoprotein, GP2; C2G4 variable Fab…
- UniProt
- Q05320
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Ebola surface glycoprotein, GP1 | protein | 235 | 11% helix, 29% strand | Q05320 |
| B, G, I | Ebola surface glycoprotein, GP2 | protein | 113 | 36% helix, 9% strand | Q05320 |
| H, P, Q | C2G4 variable Fab domain heavy chain | protein | 120 | 8% helix, 45% strand | — |
| L, T, U | C2G4 variable Fab domain light chain | protein | 107 | 3% helix, 47% strand | — |
| C, J, M | C13C6 variable Fab domain heavy chain | protein | 121 | 11% helix, 50% strand | — |
| D, N, O | C13C6 variable Fab domain light chain | protein | 107 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, D, B, H, E, N, G, P, F, O, I, Q, C, J, M
- BMA · beta-D-mannopyranose · sugar · 9 copies
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains G, I, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.87 | 0.88 | 95 | empty |
| 2 | 134 | 0.75 | 0.94 | 28 | empty |
| 3 | 194 | 0.75 | 0.91 | 32 | empty |
| 4 | 64 | 0.73 | 0.98 | 24 | empty |
| 5 | 63 | 0.72 | 0.97 | 24 | empty |
Interfaces
36 interfaces between chains.
- A–B · 2407 Ų buried · 36 hydrogen bonds · protein-protein
- F–I · 2406 Ų buried · 36 hydrogen bonds · protein-protein
- E–G · 2404 Ų buried · 36 hydrogen bonds · protein-protein
- G–I · 1037 Ų buried · 12 hydrogen bonds · protein-protein
- B–I · 1036 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 5KEL · EBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6 · 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 Q05320
- Elsewhere: RCSB PDB 5KEL · PDBe 5KEL · UniProt Q05320
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