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Crystal structure of rhesus macaque (macaca mulatta) IGG1 Fc fragment- Fc-gamma receptor III complex V158 mutant
Analyse Crystal structure of rhesus macaque (macaca mulatta) IGG1 Fc fragment- Fc-gamma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KCZ
- Type
- protein
- Length
- 1,179 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 Fc; Low affinity immunoglobulin gamma Fc region receptor III
- UniProt
- F6RL33, A3RFZ7
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | IGG1 Fc | protein | 209 | 10% helix, 45% strand | F6RL33 |
| B, E | IGG1 Fc | protein | 212 | 10% helix, 35% strand | F6RL33 |
| C | Low affinity immunoglobulin gamma Fc region receptor III | protein | 168 | 0% helix, 39% strand | A3RFZ7 |
| F | Low affinity immunoglobulin gamma Fc region receptor III | protein | 169 | 2% helix, 39% strand | A3RFZ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, C, B, D, F, E
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, D, E
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.56 | 0.76 | 30 | empty |
| 2 | 77 | 0.44 | 0.80 | 17 | empty |
| 3 | 63 | 0.35 | 0.78 | 13 | empty |
| 4 | 59 | 0.33 | 0.77 | 12 | empty |
| 5 | 78 | 0.32 | 0.74 | 20 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1242 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1155 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 543 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 521 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 339 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7KCZ · Crystal structure of rhesus macaque (macaca mulatta) IGG1 Fc fragment- Fc-gamma receptor… · the same entry in another collection · chain F against F, TM-score 1.00
- A3RFZ7 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin gamma Fc region… · a predicted model of the same protein · chain F 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 F6RL33
- Every structure of UniProt A3RFZ7
- Elsewhere: RCSB PDB 7KCZ · PDBe 7KCZ · UniProt F6RL33 · UniProt A3RFZ7
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