Research workbench
Structure of fcgammari in complex with Fc reveals the importance of glycan recognition for high affinity IgG binding
Analyse Structure of fcgammari in complex with Fc reveals the importance of glycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X4M
- Type
- protein
- Length
- 1,377 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; High affinity immunoglobulin gamma Fc receptor I
- UniProt
- P01857, P12314
- Ligands
- NAG, MAN, BMA, FUL, GAL, SIA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 218 | 11% helix, 43% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 216 | 11% helix, 44% strand | P01857 |
| C | Ig gamma-1 chain C region | protein | 212 | 11% helix, 44% strand | P01857 |
| D | Ig gamma-1 chain C region | protein | 214 | 11% helix, 44% strand | P01857 |
| E | High affinity immunoglobulin gamma Fc receptor I | protein | 259 | 5% helix, 39% strand | P12314 |
| F | High affinity immunoglobulin gamma Fc receptor I | protein | 258 | 5% helix, 40% strand | P12314 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, E, B, C, F, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.73 | 0.81 | 53 | empty |
| 2 | 729 | 0.69 | 0.76 | 69 | empty |
| 3 | 445 | 0.62 | 0.76 | 55 | NAG |
| 4 | 379 | 0.60 | 0.77 | 40 | empty |
| 5 | 74 | 0.60 | 0.89 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1161 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1161 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 796 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 622 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 569 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 4X4M · Structure of FcgammaRI in complex with Fc reveals the importance of glycan recognition… · the same entry in another collection · chain F against F, TM-score 1.00
- P12314 · AlphaFold monomer V2.0 prediction for high affinity immunoglobulin gamma Fc receptor I… · a predicted model of the same protein · chain E against A, TM-score 0.92
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
- Every structure of UniProt P12314
- Elsewhere: RCSB PDB 4X4M · PDBe 4X4M · UniProt P01857 · UniProt P12314
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.