MolNFT v1 · #83478 · protein
Crystal structure of iib selective Fc variant, FC(V12), in complex with fcgriib
3WJL · Ig gamma-1 chain C region: “Crystal structure of iib selective Fc variant, FC(V12), in complex with fcgriib”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 4 pockets (best druggability 0.50). MolNFT v1 #83478 on GenesisL1: 3D…
- PDB
- 3WJL
- Type
- protein
- Length
- 580 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-C
- UniProt
- P01857, P31995
- Ligands
- NAG, MAN, BMA, GAL, FUL
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 212 | 12% helix, 46% strand | P01857 |
| B | Ig gamma-1 chain C region | protein | 208 | 13% helix, 48% strand | P01857 |
| C | Low affinity immunoglobulin gamma Fc region receptor II-C | protein | 160 | 6% helix, 53% strand | P31995 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUL · beta-L-fucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.50 | 0.82 | 20 | empty |
| 2 | 58 | 0.30 | 0.76 | 16 | empty |
| 3 | 66 | 0.29 | 0.74 | 17 | empty |
| 4 | 64 | 0.27 | 0.72 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1161 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 421 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3WJL · Crystal structure of IIb selective Fc variant, Fc(V12), in complex with FcgRIIb · the same entry in another collection · chain A against A, TM-score 1.00
- P31995 · 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 0.99
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 P31995
- Elsewhere: RCSB PDB 3WJL · PDBe 3WJL · UniProt P01857 · UniProt P31995
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