MolNFT v1 · #78079 · protein
Complex of fcgammariia (CD32) and the Fc of human IGG1
3RY6 · Ig gamma-1 chain C region: “Complex of fcgammariia (CD32) and the Fc of human IGG1”. X-ray diffraction, 7 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.63). MolNFT v1 #78079 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3RY6
- Type
- protein
- Length
- 595 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; Low affinity immunoglobulin gamma Fc region receptor II-a
- UniProt
- P01857, P12318
- Ligands
- NAG, MAN, BMA, GAL, SIA, FUL, NDG
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ig gamma-1 chain C region | protein | 214 | 6% helix, 15% strand | P01857 |
| C | Low affinity immunoglobulin gamma Fc region receptor II-a | protein | 167 | 2% helix, 13% strand | P12318 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.63 | 0.80 | 42 | empty |
| 2 | 153 | 0.60 | 0.84 | 37 | empty |
| 3 | 150 | 0.56 | 0.81 | 33 | empty |
| 4 | 134 | 0.47 | 0.78 | 26 | empty |
| 5 | 156 | 0.42 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1296 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3RY6 · Complex of fcgammariia (CD32) and the FC of human IGG1 · the same entry in another collection · chain A against A, TM-score 1.00
- P12318 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin gamma Fc region… · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P12318
- Elsewhere: RCSB PDB 3RY6 · PDBe 3RY6 · UniProt P01857 · UniProt P12318
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