Research workbench
Fc heterodimer design 8.1 L368V/Y407A + T366V/K409F
Analyse Fc heterodimer design 8.1 L368V/Y407A + T366V/K409F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJC
- Type
- protein
- Length
- 853 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; Fc-III peptide
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, GAL, FUC, IOD
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ig gamma-1 chain C region | protein | 207 | 10% helix, 48% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 206 | 10% helix, 49% strand | P01857 |
| C, F | Fc-III peptide | protein | 13 | 0% helix, 69% strand | — |
| E | Ig gamma-1 chain C region | protein | 207 | 10% helix, 47% strand | P01857 |
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 A, D, B, E
- IOD · Iodide ion · ion · chains D
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 | 459 | 0.70 | 0.81 | 53 | empty |
| 2 | 95 | 0.48 | 0.81 | 24 | empty |
| 3 | 112 | 0.46 | 0.79 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1102 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1097 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 666 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 367 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5DJC · Fc Heterodimer Design 8.1 L368V/Y407A + T366V/K409F · 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 5DJC · PDBe 5DJC · UniProt P01857
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