Research workbench
High-resolution crystal structure of Fc bound to its human receptor Fc-gamma-ri
Analyse High-resolution crystal structure of Fc bound to its human receptor Fc-gamma-ri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W4O
- Type
- protein
- Length
- 683 residues
- Chains
- 3
- 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, GAL, FUC, ZN
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 215 | 10% helix, 47% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 209 | 11% helix, 48% strand | P01857 |
| C | High affinity immunoglobulin gamma Fc receptor I | protein | 259 | 5% helix, 52% strand | P12314 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- ACT · Acetate ion · additive · 9 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.47 | 0.74 | 21 | empty |
| 2 | 74 | 0.37 | 0.77 | 20 | empty |
| 3 | 67 | 0.28 | 0.73 | 22 | empty |
| 4 | 52 | 0.28 | 0.75 | 16 | GOL |
| 5 | 57 | 0.27 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1205 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 671 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4W4O · High-resolution crystal structure of Fc bound to its human receptor Fc-gamma-RI · the same entry in another collection · chain A against A, 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 C 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 4W4O · PDBe 4W4O · UniProt P01857 · UniProt P12314
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