Research workbench
Bundibugyo virus gp (mucin deleted) bound to antibody Fab bdbv-43
Analyse Bundibugyo virus gp (mucin deleted) bound to antibody Fab bdbv-43 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KEW
- Type
- protein
- Length
- 1,650 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein 1; Bdbv-43 Fab heavy chain; Bdbv-43 Fab light chain; Envelope…
- UniProt
- A0A510C2V9, B8XCN0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein 1 | protein | 227 | 10% helix, 40% strand | A0A510C2V9 |
| G, H, I | Bdbv-43 Fab heavy chain | protein | 122 | 8% helix, 48% strand | — |
| J, K, L | Bdbv-43 Fab light chain | protein | 106 | 3% helix, 47% strand | — |
| D, E, F | Envelope glycoprotein 2 | protein | 95 | 40% helix, 21% strand | B8XCN0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, A, D, E, C, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.87 | 0.88 | 96 | empty |
| 2 | 59 | 0.72 | 0.98 | 23 | empty |
| 3 | 98 | 0.71 | 0.93 | 19 | empty |
| 4 | 93 | 0.71 | 0.94 | 22 | empty |
| 5 | 93 | 0.70 | 0.93 | 20 | empty |
Interfaces
24 interfaces between chains.
- B–E · 2492 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2488 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 2488 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1008 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1006 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7KEW · Bundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-43 · 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 A0A510C2V9
- Every structure of UniProt B8XCN0
- Elsewhere: RCSB PDB 7KEW · PDBe 7KEW · UniProt A0A510C2V9 · UniProt B8XCN0
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