Research workbench
Crystal structure of gasdalie IGG1 Fc in complex with fcgriiia
Analyse Crystal structure of gasdalie IGG1 Fc in complex with fcgriiia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6D
- Type
- protein
- Length
- 574 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 III-a
- UniProt
- P01857, P08637
- Ligands
- NAG, MAN, BMA, GAL, FUL, FUC
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 209 | 11% helix, 46% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 208 | 9% helix, 44% strand | P01857 |
| C | Low affinity immunoglobulin gamma Fc region receptor III-a | protein | 157 | 6% helix, 49% strand | P08637 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, B
- 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 · chains A
- FUC · alpha-L-fucopyranose · sugar · chains 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 | 53 | 0.52 | 0.88 | 16 | empty |
| 2 | 57 | 0.30 | 0.76 | 16 | empty |
| 3 | 58 | 0.27 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1145 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 357 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5D6D · Crystal structure of GASDALIE IgG1 Fc in complex with FcgRIIIa · 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 0.98
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 P01857
- Every structure of UniProt P08637
- Elsewhere: RCSB PDB 5D6D · PDBe 5D6D · UniProt P01857 · UniProt P08637
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