MolNFT v1 · #124416 · protein
Ebov gp in complex with variable Fab domains of iggs C2G4 and C13C6
5KEL · Ebola surface glycoprotein, GP1: “Ebov gp in complex with variable Fab domains of iggs C2G4 and C13C6”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.87). MolNFT v1 #124416 on GenesisL1: 3D…
- 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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