Research workbench
Ebola virus makona variant gp (mucin-deleted) in complex with pan- ebolavirus human antibody adi-15878 Fab
Analyse Ebola virus makona variant gp (mucin-deleted) in complex with pan- ebolavirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DZL
- Type
- protein
- Length
- 1,587 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ebola virus makona GP1; Ebola virus makona GP2; Fv domain of adi-15878 Fab light chain…
- UniProt
- A0A0F7IM40, P87666
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ebola virus makona GP1 | protein | 213 | 11% helix, 31% strand | A0A0F7IM40 |
| D, E, F | Ebola virus makona GP2 | protein | 89 | 40% helix, 6% strand | P87666 |
| J, K, L | Fv domain of adi-15878 Fab light chain | protein | 106 | 3% helix, 46% strand | — |
| G, H, I | Fv domain of adi-15878 Fab heavy chain | protein | 121 | 5% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, D, G, B, E, H, C, F, I
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, G, J, B, H, K, C, I, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.85 | 0.85 | 107 | empty |
| 2 | 374 | 0.82 | 0.91 | 50 | empty |
| 3 | 1079 | 0.79 | 0.80 | 97 | empty |
| 4 | 1078 | 0.79 | 0.80 | 101 | empty |
| 5 | 178 | 0.78 | 0.94 | 32 | empty |
Interfaces
30 interfaces between chains.
- B–E · 2395 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 2391 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 2388 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 759 Ų buried · 1 hydrogen bond · protein-protein
- E–F · 756 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6DZL · Ebola virus Makona variant GP (mucin-deleted) in complex with pan-ebolavirus human… · the same entry in another collection · chain E against E, 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 A0A0F7IM40
- Every structure of UniProt P87666
- Elsewhere: RCSB PDB 6DZL · PDBe 6DZL · UniProt A0A0F7IM40 · UniProt P87666
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