Research workbench
Crystal structure of ebola zaire envelope glycoprotein gp in complex with compound ARN0074953
Analyse Crystal structure of ebola zaire envelope glycoprotein gp in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M2D
- Type
- protein
- Length
- 358 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GP1; GP2
- UniProt
- Q05320
- Ligands
- YPS, NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GP1 | protein | 237 | 11% helix, 38% strand | Q05320 |
| B | GP2 | protein | 121 | 42% helix, 11% strand | Q05320 |
Ligands and binding sites
- YPS · (1R,3S,5R,7R)-N-[(1r,4R)-4-aminocyclohexyl]-3-(ethoxymethyl)-5-phenyladamantane-1-carboxamide · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.59 | 0.80 | 25 | YPS |
| 2 | 174 | 0.58 | 0.81 | 28 | empty |
| 3 | 99 | 0.46 | 0.80 | 27 | empty |
| 4 | 97 | 0.38 | 0.75 | 16 | empty |
| 5 | 70 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2685 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7M2D · Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound… · 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 7M2D · PDBe 7M2D · UniProt Q05320
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