Research workbench
Crystal structure of the complex between AFUCOSYLATED/GALACTOSYLATED human IGG1 Fc and Fc gamma receptor iiia (CD16A) with MAN5 N-glycans
Analyse Crystal structure of the complex between AFUCOSYLATED/GALACTOSYLATED human IGG1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VU0
- Type
- protein
- Length
- 596 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain; Low affinity immunoglobulin gamma Fc region receptor…
- UniProt
- P0DOX5, H0Y755
- Ligands
- NAG, MAN, BMA, GAL, NA
- Pockets
- 4 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain | protein | 215 | 10% helix, 46% strand | P0DOX5 |
| B | Immunoglobulin gamma-1 heavy chain | protein | 216 | 11% helix, 45% strand | P0DOX5 |
| C | Low affinity immunoglobulin gamma Fc region receptor III-a | protein | 165 | 5% helix, 55% strand | H0Y755 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 9 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- 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
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.34 | 0.73 | 26 | EDO |
| 2 | 78 | 0.34 | 0.75 | 22 | empty |
| 3 | 60 | 0.32 | 0.77 | 17 | empty |
| 4 | 55 | 0.28 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1346 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 578 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 365 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5VU0 · Crystal structure of the complex between afucosylated/galactosylated human IgG1 Fc and Fc… · the same entry in another collection · chain A against A, TM-score 1.00
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 P0DOX5
- Every structure of UniProt H0Y755
- Elsewhere: RCSB PDB 5VU0 · PDBe 5VU0 · UniProt P0DOX5 · UniProt H0Y755
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