MolNFT v1 · #161395 · protein
EM structure of a ebov-gp bound to 4M0368 neutralizing antibody
6QD8 · Light chain: “EM structure of a ebov-gp bound to 4M0368 neutralizing antibody”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #161395 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6QD8
- Type
- protein
- Length
- 1,812 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Envelope GLYCOPROTEIN,VIRION spike GLYCOPROTEIN,EBOV-GP1; Envelope…
- UniProt
- Q05320
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Z, Y, L | Light chain | protein | 104 | 0% helix, 43% strand | — |
| A, C, E | Envelope GLYCOPROTEIN,VIRION spike GLYCOPROTEIN,EBOV-GP1 | protein | 256 | 10% helix, 39% strand | Q05320 |
| B, F, D | Envelope glycoprotein | protein | 130 | 39% helix, 12% strand | Q05320 |
| H, W, Q | Heavy chain | protein | 114 | 0% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, H, E, F, W, C, D, Q
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.84 | 0.90 | 71 | empty |
| 2 | 200 | 0.82 | 0.95 | 25 | empty |
| 3 | 248 | 0.77 | 0.90 | 32 | empty |
| 4 | 70 | 0.70 | 0.96 | 21 | empty |
| 5 | 139 | 0.70 | 0.90 | 30 | empty |
Interfaces
33 interfaces between chains.
- E–F · 2850 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2834 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2829 Ų buried · 23 hydrogen bonds · protein-protein
- F–D · 1227 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1221 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6QD8 · EM structure of a EBOV-GP bound to 4M0368 neutralizing antibody · the same entry in another collection · chain F against F, 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 6QD8 · PDBe 6QD8 · UniProt Q05320
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