MolNFT v1 · #22540 · protein
Crystal structure of a human type III Fc gamma receptor in complex with an Fc fragment of IGG1 (hexagonal)
1T89 · Recombinant IGG1 heavy chain: “Crystal structure of a human type III Fc gamma receptor in complex with an Fc fragment of IGG1 (hexagonal)”. X-ray diffraction, 7 ligands (NAG, BMA, MAN), 3 pockets (best druggability 0.35). MolNFT v1…
- PDB
- 1T89
- Type
- protein
- Length
- 590 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recombinant IGG1 heavy chain; Low affinity immunoglobulin gamma Fc region receptor III-B
- UniProt
- O75015
- Ligands
- NAG, BMA, MAN, NDG, GAL, FUL, FUC
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Recombinant IGG1 heavy chain | protein | 210 | 6% helix, 41% strand | — |
| B | Recombinant IGG1 heavy chain | protein | 213 | 9% helix, 37% strand | — |
| C | Low affinity immunoglobulin gamma Fc region receptor III-B | protein | 167 | 4% helix, 49% strand | O75015 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A
- FUL · beta-L-fucopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.35 | 0.80 | 16 | empty |
| 2 | 85 | 0.34 | 0.75 | 21 | empty |
| 3 | 54 | 0.28 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1198 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1T89 · Crystal structure of a human type III Fc gamma receptor in complex with an Fc fragment of… · the same entry in another collection · chain A against A, TM-score 1.00
- O75015 · 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 0.96
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 O75015
- Elsewhere: RCSB PDB 1T89 · PDBe 1T89 · UniProt O75015
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