MolNFT v2 · #116936 · protein
Fc Heterodimer Design 20.8 Y349S/T366V/K370Y/K409V + E357D/S364Q/Y407A
5DJY · Ig gamma-1 chain C region: “Fc Heterodimer Design 20.8 Y349S/T366V/K370Y/K409V + E357D/S364Q/Y407A”. X-ray diffraction at 2.15, 5 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.36). MolNFT v2 #116936 on GenesisL1: 3D…
- PDB
- 5DJY
- Type
- protein
- Length
- 428 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Ig gamma-1 chain C region; Fc-III peptide
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · resolution 2.15 · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 208 | 9% helix, 49% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 207 | 9% helix, 48% strand | P01857 |
| C | Fc-III peptide | protein | 13 | 0% helix, 69% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, 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
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.36 | 0.77 | 17 | empty |
| 2 | 59 | 0.30 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1056 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 659 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5DJY · Fc heterodimer design 20.8 Y349S/T366V/K370Y/K409V + E357D/S364Q/Y407A · 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 5DJY · PDBe 5DJY · UniProt P01857
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