MolNFT v1 · #121537 · protein
Glycosylated, disulfide-linked hole-hole Fc fragment
5HYI · Ig gamma-1 chain C region: “Glycosylated, disulfide-linked hole-hole Fc fragment”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 6 pockets (best druggability 0.75). MolNFT v1 #121537 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HYI
- Type
- protein
- Length
- 835 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 209 | 8% helix, 50% strand | P01857 |
| B, D | Ig gamma-1 chain C region | protein | 209 | 9% helix, 49% strand | P01857 |
| C | Ig gamma-1 chain C region | protein | 208 | 10% helix, 50% strand | P01857 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, C, 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 | 1137 | 0.75 | 0.78 | 95 | empty |
| 2 | 73 | 0.36 | 0.77 | 21 | empty |
| 3 | 67 | 0.33 | 0.76 | 18 | empty |
| 4 | 68 | 0.29 | 0.74 | 18 | empty |
| 5 | 56 | 0.27 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1121 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1090 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 813 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 190 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5HYI · Glycosylated, disulfide-linked Hole-Hole Fc fragment · 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 P01857
- Elsewhere: RCSB PDB 5HYI · PDBe 5HYI · UniProt P01857
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