Research workbench
Neonatal Fc receptor, pH 6.5
Analyse Neonatal Fc receptor, pH 6.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FRU
- Type
- protein
- Length
- 1,104 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neonatal Fc receptor; Beta-2-microglobulin
- UniProt
- P13599, P07151
- Ligands
- NAG, NDG, BMA, MAN, GAL, FUL, FUC, SO4
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Neonatal Fc receptor | protein | 269 | 27% helix, 40% strand | P13599 |
| B, D, F | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P07151 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains C, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains C, A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains C, A
- FUL · beta-L-fucopyranose · sugar · chains C
- FUC · alpha-L-fucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, D, C
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.74 | 0.77 | 80 | SO4 |
| 2 | 1062 | 0.73 | 0.76 | 80 | BME |
| 3 | 1032 | 0.72 | 0.76 | 88 | BME |
| 4 | 487 | 0.64 | 0.77 | 47 | BME |
| 5 | 151 | 0.56 | 0.82 | 22 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1508 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1505 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1494 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 509 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 503 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3FRU · Neonatal Fc receptor, pH 6.5 · the same entry in another collection · chain F against F, 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 C against A, TM-score 0.99
- P07151 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P07151) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 3FRU · PDBe 3FRU · UniProt P13599 · UniProt P07151
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