Research workbench
Ebov gpdmuc makona bound to rebov-548 Fab
Analyse Ebov gpdmuc makona bound to rebov-548 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UYE
- Type
- protein
- Length
- 1,686 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sgp; Virion spike glycoprotein; Antibody rebov-548 Fab, heavy chain; Antibody rebov-548…
- UniProt
- A0A1C4HDL5, A0A1C4HDV6
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 12% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Sgp | protein | 231 | 9% helix, 35% strand | A0A1C4HDL5 |
| D, E, F | Virion spike glycoprotein | protein | 91 | 41% helix, 18% strand | A0A1C4HDV6 |
| G, H, I | Antibody rebov-548 Fab, heavy chain | protein | 132 | 7% helix, 49% strand | — |
| J, K, L | Antibody rebov-548 Fab, light chain | protein | 108 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, G, D, B, H, E, C, I, F
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 6 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.88 | 0.89 | 123 | empty |
| 2 | 633 | 0.71 | 0.79 | 68 | empty |
| 3 | 593 | 0.71 | 0.79 | 68 | empty |
| 4 | 598 | 0.70 | 0.78 | 59 | empty |
| 5 | 89 | 0.67 | 0.92 | 22 | empty |
Interfaces
24 interfaces between chains.
- B–E · 2686 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 2686 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2679 Ų buried · 27 hydrogen bonds · protein-protein
- I–L · 875 Ų buried · 5 hydrogen bonds · protein-protein
- G–J · 864 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6UYE · EBOV GPdMuc Makona bound to rEBOV-548 Fab · 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 A0A1C4HDL5
- Every structure of UniProt A0A1C4HDV6
- Elsewhere: RCSB PDB 6UYE · PDBe 6UYE · UniProt A0A1C4HDL5 · UniProt A0A1C4HDV6
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