MolNFT v1 · #127053 · protein
Cocrystal structure of Fc gamma receptor iiia interacting with affimer F4, a specific binding protein which blocks IgG binding to the receptor.
5ML9 · Low affinity immunoglobulin gamma Fc region receptor III-a: “Cocrystal structure of Fc gamma receptor iiia interacting with affimer F4, a specific binding protein which…”. X-ray diffraction, 3 ligands (NAG, SO4, CL), 3 pockets (best…
- PDB
- 5ML9
- Type
- protein
- Length
- 275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low affinity immunoglobulin gamma Fc region receptor III-a; Affimer F4 with specificity…
- UniProt
- P08637
- Ligands
- NAG, SO4, CL
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low affinity immunoglobulin gamma Fc region receptor III-a | protein | 172 | 3% helix, 51% strand | P08637 |
| B | Affimer F4 with specificity for Fc gamma receptor iiia | protein | 103 | 18% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
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 | 73 | 0.41 | 0.80 | 13 | empty |
| 2 | 78 | 0.33 | 0.75 | 23 | SO4 |
| 3 | 86 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 984 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5ML9 · Cocrystal structure of Fc gamma receptor IIIa interacting with Affimer F4, a specific… · the same entry in another collection · chain A against A, TM-score 1.00
- P08637 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin gamma Fc region… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P08637
- Elsewhere: RCSB PDB 5ML9 · PDBe 5ML9 · UniProt P08637
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