Research workbench
Crystal structure of the complex of rat neonatal Fc receptor with Fc
Analyse Crystal structure of the complex of rat neonatal Fc receptor with Fc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FRT
- Type
- protein
- Length
- 573 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neonatal Fc receptor; Beta 2-microglobulin; IgG Fc
- UniProt
- P13599, P07151
- Ligands
- NAG, FUC, MAN, BMA, GAL
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neonatal Fc receptor | protein | 269 | 27% helix, 40% strand | P13599 |
| B | Beta 2-microglobulin | protein | 99 | 0% helix, 49% strand | P07151 |
| C | IgG Fc | protein | 205 | 9% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains C
- BMA · beta-D-mannopyranose · sugar · chains C
- GAL · beta-D-galactopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.64 | 0.77 | 44 | empty |
| 2 | 89 | 0.56 | 0.85 | 18 | empty |
| 3 | 119 | 0.50 | 0.80 | 21 | empty |
| 4 | 129 | 0.47 | 0.78 | 21 | empty |
| 5 | 177 | 0.47 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1571 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 684 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1FRT · Crystal structure of the complex of rat neonatal Fc receptor with Fc · the same entry in another collection · chain A against A, TM-score 1.00
- P13599 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P13599) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P07151 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P07151) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P13599
- Every structure of UniProt P07151
- Elsewhere: RCSB PDB 1FRT · PDBe 1FRT · UniProt P13599 · UniProt P07151
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