MolNFT v1 · #109502 · protein
Structure of fcgammari in complex with Fc reveals the importance of glycan recognition for high affinity IgG binding
4X4M · Ig gamma-1 chain C region: “Structure of fcgammari in complex with Fc reveals the importance of glycan recognition for high affinity IgG…”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.73). MolNFT v1…
- 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
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