Research workbench
Crystal structure of a human IGG1 Fc-FRAGMENT,HIGH salt condition
Analyse Crystal structure of a human IGG1 Fc-FRAGMENT,HIGH salt condition in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H3Y
- Type
- protein
- Length
- 412 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region
- Ligands
- NAG, MAN, GLA, FUL, BMA
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ig gamma-1 chain C region | protein | 206 | 10% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.67 | 0.86 | 49 | empty |
| 2 | 129 | 0.64 | 0.87 | 33 | empty |
| 3 | 51 | 0.60 | 0.92 | 20 | empty |
| 4 | 68 | 0.57 | 0.89 | 23 | empty |
| 5 | 81 | 0.55 | 0.86 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 876 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1H3Y · Crystal structure of a human IgG1 Fc-fragment,high salt condition · 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
- Elsewhere: RCSB PDB 1H3Y · PDBe 1H3Y
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