Research workbench
Unique carbohydrate-carbohydrate interactions are required for high affinity binding between fcgiii and antibodies lacking core fucose
Analyse Unique carbohydrate-carbohydrate interactions are required for high affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SGJ
- Type
- protein
- Length
- 605 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human Fc fragment; Human FCG3A receptor
- UniProt
- P01857, P08637
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 2 · best druggability 0.29
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human Fc fragment | protein | 219 | 12% helix, 45% strand | P01857 |
| B | Human Fc fragment | protein | 217 | 13% helix, 46% strand | P01857 |
| C | Human FCG3A receptor | protein | 169 | 5% helix, 54% strand | P08637 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.29 | 0.73 | 25 | empty |
| 2 | 63 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1334 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 559 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3SGJ · Unique carbohydrate-carbohydrate interactions are required for high affinity binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P08637 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin gamma Fc region… · a predicted model of the same protein · chain C against A, TM-score 0.92
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 P01857
- Every structure of UniProt P08637
- Elsewhere: RCSB PDB 3SGJ · PDBe 3SGJ · UniProt P01857 · UniProt P08637
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