MolNFT v1 · #125673 · protein
Room temperature structure of human IGG4-Fc from crystals analysed in situ
5LG1 · Ig gamma-4 chain C region: “Room temperature structure of human IGG4-Fc from crystals analysed in situ”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.36). MolNFT v1 #125673 on GenesisL1: 3D structure…
- PDB
- 5LG1
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-4 chain C region
- UniProt
- P01861
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-4 chain C region | protein | 209 | 11% helix, 49% strand | P01861 |
| B | Ig gamma-4 chain C region | protein | 208 | 11% helix, 48% strand | P01861 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.36 | 0.77 | 17 | empty |
| 2 | 55 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1212 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5LG1 · Room temperature structure of human IgG4-Fc from crystals analysed in situ · the same entry in another collection · chain A against A, TM-score 1.00
- P01861 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 4 (P01861) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P01861
- Elsewhere: RCSB PDB 5LG1 · PDBe 5LG1 · UniProt P01861
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