MolNFT v1 · #116611 · protein
Fc heterodimer design 7.4 Y407A + T366V/K409V
5DJ2 · Ig gamma-1 chain C region: “Fc heterodimer design 7.4 Y407A + T366V/K409V”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 1 pocket (best druggability 0.37). MolNFT v1 #116611 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5DJ2
- Type
- protein
- Length
- 428 residues
- Chains
- 3
- 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
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 208 | 10% helix, 48% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 207 | 10% helix, 49% 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 A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.37 | 0.77 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1155 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 670 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5DJ2 · Fc Heterodimer Design 7.4 Y407A + T366V/K409V · 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 5DJ2 · PDBe 5DJ2 · UniProt P01857
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