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Crystal structure of a chemoenzymatic glycoengineered disialylated Fc (di-sfc)
Analyse Crystal structure of a chemoenzymatic glycoengineered disialylated Fc (di-sfc) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q6Y
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, GAL, SIA
- Pockets
- 8 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 208 | 11% helix, 44% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 206 | 11% helix, 46% strand | P01857 |
| C | Ig gamma-1 chain C region | protein | 199 | 11% helix, 46% strand | P01857 |
| D | Ig gamma-1 chain C region | protein | 195 | 11% helix, 45% strand | P01857 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B, C, D
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.59 | 0.77 | 27 | empty |
| 2 | 284 | 0.57 | 0.77 | 44 | empty |
| 3 | 53 | 0.39 | 0.81 | 11 | empty |
| 4 | 65 | 0.31 | 0.75 | 16 | empty |
| 5 | 64 | 0.30 | 0.75 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1141 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1125 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 244 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4Q6Y · Crystal structure of a chemoenzymatic glycoengineered disialylated Fc (di-sFc) · 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 P01857
- Elsewhere: RCSB PDB 4Q6Y · PDBe 4Q6Y · UniProt P01857
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