MolNFT v1 · #138000 · protein
Crystal structure of human IGG4-SIGMA1 Fc fragment
5W5M · Immunoglobulin heavy constant gamma 4: “Crystal structure of human IGG4-SIGMA1 Fc fragment”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 4 pockets (best druggability 0.34). MolNFT v1 #138000 on GenesisL1: 3D structure, binding…
- PDB
- 5W5M
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin heavy constant gamma 4
- UniProt
- P01861
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 4 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin heavy constant gamma 4 | protein | 207 | 10% helix, 50% strand | P01861 |
| B | Immunoglobulin heavy constant gamma 4 | protein | 209 | 12% helix, 49% 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
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains 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 | 56 | 0.34 | 0.78 | 15 | empty |
| 2 | 61 | 0.31 | 0.76 | 19 | empty |
| 3 | 55 | 0.29 | 0.76 | 15 | empty |
| 4 | 58 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1148 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 5W5M · PDBe 5W5M · UniProt P01861
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