Research workbench
Crystal structure of iib selective Fc variant, FC(P238D), in complex with fcgriib
Analyse Crystal structure of iib selective Fc variant, FC(P238D), 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
- 3WJJ
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; Low affinity immunoglobulin gamma Fc region receptor II-B
- UniProt
- P01857, P31994
- Ligands
- NAG, MAN, BMA, GAL, FUL
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 212 | 11% helix, 47% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 206 | 11% helix, 48% strand | P01857 |
| C | Low affinity immunoglobulin gamma Fc region receptor II-B | protein | 164 | 2% helix, 50% strand | P31994 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.51 | 0.79 | 25 | empty |
| 2 | 55 | 0.36 | 0.79 | 18 | empty |
| 3 | 52 | 0.30 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1168 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 331 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3WJJ · Crystal structure of IIb selective Fc variant, Fc(P238D), in complex with FcgRIIb · the same entry in another collection · chain A against A, TM-score 1.00
- P31994 · 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 0.96
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 P31994
- Elsewhere: RCSB PDB 3WJJ · PDBe 3WJJ · UniProt P01857 · UniProt P31994
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