Research workbench
Crystal structure of Fc-fragment of human IGG2-sigma antibody
Analyse Crystal structure of Fc-fragment of human IGG2-sigma antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L4J
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-2 chain C region
- UniProt
- P01859
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-2 chain C region | protein | 208 | 11% helix, 49% strand | P01859 |
| B | Ig gamma-2 chain C region | protein | 182 | 13% helix, 49% strand | P01859 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.48 | 0.86 | 16 | empty |
| 2 | 59 | 0.28 | 0.74 | 16 | empty |
| 3 | 73 | 0.28 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1158 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4L4J · Crystal structure of fc-fragment of human IgG2-Sigma antibody · the same entry in another collection · chain A against A, TM-score 1.00
- P01859 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 2 (P01859) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P01859
- Elsewhere: RCSB PDB 4L4J · PDBe 4L4J · UniProt P01859
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