Research workbench
Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated soluble form of Fc gamma receptor IIIa
Analyse Crystal structure of fucosylated IgG1 Fc complexed with bis-glycosylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XJE
- Type
- protein
- Length
- 577 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- Immunoglobulin gamma-1 heavy chain; Low affinity immunoglobulin gamma Fc region receptor…
- UniProt
- P0DOX5, P08637
- Ligands
- NAG, MAN, BMA, FUC, GAL, CL
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain | protein | 213 | 11% helix, 46% strand | P0DOX5 |
| B | Immunoglobulin gamma-1 heavy chain | protein | 215 | 11% helix, 46% strand | P0DOX5 |
| C | Low affinity immunoglobulin gamma Fc region receptor III-A | protein | 149 | 6% helix, 50% strand | P08637 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.47 | 0.76 | 31 | empty |
| 2 | 142 | 0.39 | 0.73 | 31 | empty |
| 3 | 90 | 0.32 | 0.73 | 25 | empty |
| 4 | 75 | 0.31 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1179 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 590 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 396 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XJE · Crystal structure of fucosylated IGG1 Fc complexed with bis- glycosylated soluble form of… · the same entry in another collection · chain A against A, TM-score 1.00
- P0DOX5 · AlphaFold monomer V2.0 prediction for immunoglobulin gamma-1 heavy chain (P0DOX5) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.98
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 P0DOX5
- Every structure of UniProt P08637
- Elsewhere: RCSB PDB 5XJE · PDBe 5XJE · UniProt P0DOX5 · UniProt P08637
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