MolNFT v1 · #168658 · protein
Next generation monomeric IGG4 Fc
6WNA · IgG receptor fcrn large subunit P51: “Next generation monomeric IGG4 Fc”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.62). MolNFT v1 #168658 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6WNA
- Type
- protein
- Length
- 563 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG receptor fcrn large subunit P51; Beta-2-microglobulin; Immunoglobulin heavy constant…
- UniProt
- P55899, P61769, P01861
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IgG receptor fcrn large subunit P51 | protein | 264 | 27% helix, 43% strand | P55899 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| H | Immunoglobulin heavy constant gamma 4 | protein | 200 | 9% helix, 49% strand | P01861 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains H
- BMA · beta-D-mannopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains H
- FUC · alpha-L-fucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.62 | 0.78 | 42 | empty |
| 2 | 387 | 0.62 | 0.77 | 54 | empty |
| 3 | 52 | 0.40 | 0.81 | 16 | empty |
| 4 | 86 | 0.37 | 0.76 | 16 | empty |
| 5 | 50 | 0.35 | 0.79 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1606 Ų buried · 25 hydrogen bonds · protein-protein
- A–H · 551 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6WNA · Next generation monomeric IgG4 Fc · the same entry in another collection · chain A against A, TM-score 1.00
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01861 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 4 (P01861) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 P55899
- Every structure of UniProt P61769
- Every structure of UniProt P01861
- Elsewhere: RCSB PDB 6WNA · PDBe 6WNA · UniProt P55899 · UniProt P61769 · UniProt P01861
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.