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Crystal structure of a human afucosylated IGG1 Fc expressed in tobacco plants (nicotiana benthamiana)
Analyse Crystal structure of a human afucosylated IGG1 Fc expressed in tobacco plants… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VSZ
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain
- UniProt
- P0DOX5
- Ligands
- NAG, MAN, BMA, GAL
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Immunoglobulin gamma-1 heavy chain | protein | 208 | 9% helix, 48% strand | P0DOX5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 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
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 | 66 | 0.32 | 0.76 | 14 | empty |
| 2 | 64 | 0.26 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1208 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6VSZ · Crystal structure of a human afucosylated IgG1 Fc expressed in tobacco plants (Nicotiana… · 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 P0DOX5
- Elsewhere: RCSB PDB 6VSZ · PDBe 6VSZ · UniProt P0DOX5
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