MolNFT v1 · #156919 · protein
Crystal structure of rhesus macaque (macaca mulatta) IGG1 Fc fragment- Fc-gamma receptor III complex
6MJ3: “Crystal structure of rhesus macaque (macaca mulatta) IGG1 Fc fragment- Fc-gamma receptor III complex”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 14 pockets (best druggability 0.64). MolNFT v1 #156919 on GenesisL1: 3D structure…
- PDB
- 6MJ3
- Type
- protein
- Length
- 1,174 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
- 14 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG1 Fc | protein | 207 | 4% helix, 41% strand | F6RL33 |
| B | IGG1 Fc | protein | 210 | 7% helix, 29% strand | F6RL33 |
| D | IGG1 Fc | protein | 208 | 9% helix, 39% strand | F6RL33 |
| E | IGG1 Fc | protein | 211 | 8% helix, 31% strand | F6RL33 |
| C, F | Low affinity immunoglobulin gamma Fc region receptor III | protein | 169 | 2% helix, 43% strand | A3RFZ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, C, B, D, F, E
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, D, E
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.64 | 0.76 | 49 | empty |
| 2 | 111 | 0.46 | 0.79 | 25 | empty |
| 3 | 68 | 0.46 | 0.83 | 20 | empty |
| 4 | 111 | 0.42 | 0.77 | 18 | empty |
| 5 | 123 | 0.42 | 0.76 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1287 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1191 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 376 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6MJ3 · 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 0.95
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 6MJ3 · PDBe 6MJ3 · UniProt F6RL33 · UniProt A3RFZ7
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