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Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody m102.3
Analyse Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CMG
- Type
- protein
- Length
- 860 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Hendra virus; Homo sapiens
- Molecule
- Glycoprotein G; m102.3 light chain; IgG Heavy chain
- UniProt
- O89343
- Ligands
- NAG, FUC, BMA, MAN
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.7 · 3 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein G | protein | 428 | 2% helix, 47% strand | O89343 |
| B | m102.3 light chain | protein | 206 | 3% helix, 50% strand | — |
| C | IgG Heavy chain | protein | 226 | 4% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.77 | 0.88 | 43 | empty |
| 2 | 402 | 0.61 | 0.76 | 42 | empty |
| 3 | 161 | 0.59 | 0.82 | 25 | empty |
| 4 | 65 | 0.54 | 0.88 | 24 | empty |
| 5 | 248 | 0.50 | 0.75 | 44 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1633 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 909 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6CMG · Crystal structure of the hendra virus attachment G glycoprotein bound to a potent… · 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 O89343
- Elsewhere: RCSB PDB 6CMG · PDBe 6CMG · UniProt O89343
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