Research workbench
Bdbv-289 bound to ebov gpdmuc makona
Analyse Bdbv-289 bound to ebov gpdmuc makona in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KEJ
- Type
- protein
- Length
- 1,740 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion spike glycoprotein; Antibody Fab heavy chain (hc) bdbv-289; Antibody Fab light…
- UniProt
- A0A1C4HDV6, A0A0E3XK95
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, A | Virion spike glycoprotein | protein | 235 | 12% helix, 41% strand | A0A1C4HDV6 |
| H, I, G | Antibody Fab heavy chain (hc) bdbv-289 | protein | 129 | 5% helix, 57% strand | — |
| K, L, J | Antibody Fab light chain (lc) bdbv-289 | protein | 110 | 5% helix, 50% strand | — |
| E, F, D | Virion spike glycoprotein | protein | 106 | 39% helix, 17% strand | A0A0E3XK95 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, E, F, C, D, A
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, F, C, D, E, A
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.85 | 0.86 | 107 | empty |
| 2 | 96 | 0.74 | 0.96 | 22 | empty |
| 3 | 89 | 0.73 | 0.96 | 23 | empty |
| 4 | 93 | 0.71 | 0.94 | 22 | empty |
| 5 | 63 | 0.69 | 0.96 | 18 | empty |
Interfaces
24 interfaces between chains.
- B–E · 2686 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2681 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2677 Ų buried · 28 hydrogen bonds · protein-protein
- A–G · 1070 Ų buried · 9 hydrogen bonds · protein-protein
- C–I · 1066 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7KEJ · BDBV-289 bound to EBOV GPdMuc Makona · the same entry in another collection · chain B against B, 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 7KEJ · PDBe 7KEJ · UniProt A0A1C4HDV6 · UniProt A0A0E3XK95
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.