Research workbench
Crystal structure of deglycosylated serum-derived human IGG4 Fc
Analyse Crystal structure of deglycosylated serum-derived human IGG4 Fc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D2N
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-4 chain C region
- UniProt
- P01861
- Pockets
- 12 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-4 chain C region | protein | 208 | 10% helix, 50% strand | P01861 |
| B | Ig gamma-4 chain C region | protein | 206 | 11% helix, 51% strand | P01861 |
| C | Ig gamma-4 chain C region | protein | 205 | 11% helix, 49% strand | P01861 |
| D | Ig gamma-4 chain C region | protein | 209 | 10% helix, 49% strand | P01861 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.48 | 0.75 | 34 | empty |
| 2 | 227 | 0.44 | 0.72 | 33 | empty |
| 3 | 100 | 0.40 | 0.76 | 26 | empty |
| 4 | 111 | 0.39 | 0.75 | 22 | empty |
| 5 | 143 | 0.39 | 0.73 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1162 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1135 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 338 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 302 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4D2N · Crystal structure of deglycosylated serum-derived human IgG4 Fc · the same entry in another collection · chain D against D, TM-score 1.00
- P01861 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 4 (P01861) · 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 P01861
- Elsewhere: RCSB PDB 4D2N · PDBe 4D2N · UniProt P01861
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