MolNFT v1 · #6939 · protein
Crystal structure of the complex of rat neonatal Fc receptor with Fc
1FRT: “Crystal structure of the complex of rat neonatal Fc receptor with Fc”. X-ray diffraction, 5 ligands (NAG, FUC, MAN), 9 pockets (best druggability 0.64). MolNFT v1 #6939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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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