Research workbench
EM structure of a ebov-gp bound to 3T0331 neutralizing antibody
Analyse EM structure of a ebov-gp bound to 3T0331 neutralizing antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QD7
- Type
- protein
- Length
- 1,842 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain; Envelope GLYCOPROTEIN,VIRION spike GLYCOPROTEIN,EBOV-GP1…
- UniProt
- Q05320
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, Z, P | Light chain | protein | 108 | 3% helix, 50% strand | — |
| H, X, U | Heavy chain | protein | 120 | 10% helix, 51% strand | — |
| A, C, E | Envelope GLYCOPROTEIN,VIRION spike GLYCOPROTEIN,EBOV-GP1 | protein | 256 | 10% helix, 39% strand | Q05320 |
| B, D, F | Envelope glycoprotein | protein | 130 | 42% helix, 11% strand | Q05320 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, F, B, C, E, D
- 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 | 682 | 0.86 | 0.90 | 80 | empty |
| 2 | 123 | 0.77 | 0.95 | 26 | empty |
| 3 | 226 | 0.75 | 0.89 | 33 | empty |
| 4 | 143 | 0.70 | 0.90 | 34 | empty |
| 5 | 90 | 0.70 | 0.94 | 28 | empty |
Interfaces
27 interfaces between chains.
- E–F · 2816 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2801 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2796 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1305 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1252 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6QD7 · EM structure of a EBOV-GP bound to 3T0331 neutralizing antibody · the same entry in another collection · chain L against L, 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 6QD7 · PDBe 6QD7 · UniProt Q05320
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