MolNFT v1 · #116583 · protein
Fc knob-hole heterodimer T366W + T366S/L368A/Y407V
5DI8 · Ig gamma-1 chain C region: “Fc knob-hole heterodimer T366W + T366S/L368A/Y407V”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 1 pocket (best druggability 0.30). MolNFT v1 #116583 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DI8
- 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 0.30
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, 49% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 207 | 11% helix, 47% 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 | 57 | 0.30 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1116 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 666 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5DI8 · Fc Knob-Hole Heterodimer T366W + T366S/L368A/Y407V · 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 5DI8 · PDBe 5DI8 · UniProt P01857
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