Research workbench
Bundibugyo virus gp (mucin-deleted) in complex with pan-ebolavirus human antibody adi-15878 Fab
Analyse Bundibugyo virus gp (mucin-deleted) in complex with pan-ebolavirus human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DZM
- Type
- protein
- Length
- 1,695 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bundibugyo virus GP1; Bundibugyo virus GP2; Antibody adi-15878 Fab, light chain; Antibody…
- UniProt
- B8XCN0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 13% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bundibugyo virus GP1 | protein | 224 | 8% helix, 29% strand | B8XCN0 |
| D, E, F | Bundibugyo virus GP2 | protein | 115 | 40% helix, 12% strand | B8XCN0 |
| H, K, L | Antibody adi-15878 Fab, light chain | protein | 106 | 3% helix, 42% strand | — |
| G, I, J | Antibody adi-15878 Fab, heavy chain | protein | 120 | 3% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, D, G, B, E, I, C, F, J
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains H, K, L
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.87 | 0.88 | 138 | empty |
| 2 | 619 | 0.86 | 0.90 | 92 | empty |
| 3 | 172 | 0.82 | 0.96 | 26 | empty |
| 4 | 121 | 0.80 | 0.98 | 31 | empty |
| 5 | 158 | 0.80 | 0.95 | 20 | empty |
Interfaces
33 interfaces between chains.
- C–F · 2380 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2377 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 2374 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1076 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 1076 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6DZM · Bundibugyo virus GP (mucin-deleted) in complex with pan-ebolavirus human antibody… · 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 B8XCN0
- Elsewhere: RCSB PDB 6DZM · PDBe 6DZM · UniProt B8XCN0
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