Research workbench
Fc Heterodimer Design 2.9 L368M/K370E + E357A/S364G
Analyse Fc Heterodimer Design 2.9 L368M/K370E + E357A/S364G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJX
- Type
- protein
- Length
- 856 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Ig gamma-1 chain C region; Fc-III peptide
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.25 · 3 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ig gamma-1 chain C region | protein | 208 | 10% helix, 50% strand | P01857 |
| B, E | Ig gamma-1 chain C region | protein | 207 | 11% helix, 48% strand | P01857 |
| C, F | Fc-III peptide | protein | 13 | 0% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, D, E
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, D, E
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, D, E
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, A, D, E
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 | 490 | 0.71 | 0.81 | 52 | empty |
| 2 | 100 | 0.40 | 0.77 | 17 | empty |
| 3 | 77 | 0.38 | 0.78 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1115 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1064 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 630 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 621 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 378 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5DJX · Fc heterodimer design 2.9 L368M/K370E + E357A/S364G · 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 5DJX · PDBe 5DJX · UniProt P01857
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