Research workbench
Crystal structure of the neonatal Fc receptor complexed with a heterodimeric Fc
Analyse Crystal structure of the neonatal Fc receptor complexed with a heterodimeric Fc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I1A
- Type
- protein
- Length
- 774 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neonatal Fc receptor a; Beta-2-microglobulin; Ig gamma-2A chain C region
- UniProt
- P13599, P07151, P20760
- Ligands
- CYS, NAG, MAN, FUC, BMA, NDG, FUL
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neonatal Fc receptor a | protein | 265 | 28% helix, 39% strand | P13599 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P07151 |
| C | Ig gamma-2A chain C region | protein | 205 | 10% helix, 47% strand | P20760 |
| D | Ig gamma-2A chain C region | protein | 205 | 8% helix, 35% strand | P20760 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, D
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains C, D
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains C, D
- FUL · beta-L-fucopyranose · 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 | 438 | 0.63 | 0.77 | 41 | empty |
| 2 | 217 | 0.54 | 0.77 | 19 | empty |
| 3 | 133 | 0.47 | 0.78 | 27 | empty |
| 4 | 137 | 0.44 | 0.76 | 21 | empty |
| 5 | 136 | 0.41 | 0.75 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1504 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1237 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 1I1A · Crystal structure of the neonatal Fc receptor complexed with a heterodimeric Fc · the same entry in another collection · chain D against D, 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 0.99
- P07151 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P07151) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P20760 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region (P20760) · a predicted model of the same protein · chain C 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
- Every structure of UniProt P20760
- Elsewhere: RCSB PDB 1I1A · PDBe 1I1A · UniProt P13599 · UniProt P07151 · UniProt P20760
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