Research workbench
Cleaved Ebola GP in complex with a broadly neutralizing human antibody, ADI-15946
Analyse Cleaved Ebola GP in complex with a broadly neutralizing human antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MAM
- Type
- protein
- Length
- 2,131 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.1
- Source
- Homo sapiens; Zaire ebolavirus (strain Mayinga-76)
- Molecule
- ADI-15946 Fab Heavy Chain; ADI-15946 Fab Light Chain; Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 4.1 · 10 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADI-15946 Fab Heavy Chain | protein | 226 | 7% helix, 49% strand | — |
| B, D | ADI-15946 Fab Light Chain | protein | 215 | 5% helix, 50% strand | — |
| C | ADI-15946 Fab Heavy Chain | protein | 233 | 7% helix, 47% strand | — |
| E | ADI-15946 Fab Heavy Chain | protein | 235 | 8% helix, 48% strand | — |
| F | ADI-15946 Fab Light Chain | protein | 216 | 5% helix, 50% strand | — |
| G | Envelope glycoprotein | protein | 157 | 8% helix, 44% strand | Q05320 |
| H | Envelope glycoprotein | protein | 108 | 33% helix, 12% strand | Q05320 |
| I, K | Envelope glycoprotein | protein | 156 | 8% helix, 43% strand | Q05320 |
| J | Envelope glycoprotein | protein | 109 | 33% helix, 11% strand | Q05320 |
| L | Envelope glycoprotein | protein | 105 | 34% helix, 12% strand | Q05320 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains G, H, J, I, K, L
- MAN · alpha-D-mannopyranose · sugar · 5 copies
- 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.83 | 0.84 | 113 | empty |
| 2 | 620 | 0.78 | 0.84 | 73 | empty |
| 3 | 346 | 0.74 | 0.86 | 47 | empty |
| 4 | 64 | 0.72 | 0.98 | 20 | empty |
| 5 | 60 | 0.71 | 0.98 | 19 | empty |
Interfaces
30 interfaces between chains.
- I–J · 2548 Ų buried · 36 hydrogen bonds · protein-protein
- K–L · 2521 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2515 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2047 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2041 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6MAM · Cleaved ebola gp in complex with a broadly neutralizing human antibody, adi-15946 · 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 Q05320
- Elsewhere: RCSB PDB 6MAM · PDBe 6MAM · UniProt Q05320
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