Research workbench
Cocrystal structure of Fc gamma receptor iiia interacting with affimer G3, a specific binding protein which blocks IgG binding to the receptor.
Analyse Cocrystal structure of Fc gamma receptor iiia interacting with affimer G3, a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MN2
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low affinity immunoglobulin gamma Fc region receptor III-a; Affimer G3
- UniProt
- P08637
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low affinity immunoglobulin gamma Fc region receptor III-a | protein | 172 | 3% helix, 53% strand | P08637 |
| B | Low affinity immunoglobulin gamma Fc region receptor III-a | protein | 168 | 5% helix, 52% strand | P08637 |
| C | Affimer G3 | protein | 88 | 18% helix, 65% strand | — |
| D | Affimer G3 | protein | 90 | 20% helix, 63% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.54 | 0.76 | 30 | empty |
| 2 | 102 | 0.46 | 0.80 | 17 | empty |
| 3 | 141 | 0.43 | 0.75 | 22 | empty |
| 4 | 138 | 0.41 | 0.74 | 22 | empty |
| 5 | 105 | 0.35 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–D · 743 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 251 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5MN2 · Cocrystal structure of Fc gamma receptor IIIa interacting with Affimer G3, 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 B against A, TM-score 0.85
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 5MN2 · PDBe 5MN2 · UniProt P08637
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