Research workbench
Engineered human IgG Fc domain GLYCO801 (FC801)
Analyse Engineered human IgG Fc domain GLYCO801 (FC801) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V4E
- Type
- protein
- Length
- 1,586 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, FUC, K
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 218 | 10% helix, 46% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 186 | 12% helix, 47% strand | P01857 |
| C | Ig gamma-1 chain C region | protein | 162 | 14% helix, 40% strand | P01857 |
| D | Ig gamma-1 chain C region | protein | 200 | 12% helix, 48% strand | P01857 |
| E | Ig gamma-1 chain C region | protein | 208 | 10% helix, 49% strand | P01857 |
| F | Ig gamma-1 chain C region | protein | 177 | 8% helix, 45% strand | P01857 |
| G | Ig gamma-1 chain C region | protein | 219 | 10% helix, 46% strand | P01857 |
| H | Ig gamma-1 chain C region | protein | 216 | 11% helix, 49% strand | P01857 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C, D, E, G, H, B
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, D, E, G, H, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, C, D, E, G, H
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, E, G, H
- K · Potassium ion · metal · 2 copies · chains A, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.70 | 0.79 | 70 | K |
| 2 | 591 | 0.66 | 0.76 | 58 | empty |
| 3 | 190 | 0.59 | 0.82 | 31 | empty |
| 4 | 225 | 0.58 | 0.80 | 41 | empty |
| 5 | 161 | 0.52 | 0.79 | 38 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1430 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1129 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1120 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1052 Ų buried · 6 hydrogen bonds · protein-protein
- D–G · 803 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5V4E · Engineered human IgG Fc domain glyco801 (Fc801) · 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 5V4E · PDBe 5V4E · UniProt P01857
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