MolNFT v1 · #159955 · protein
Human IGG1 Fc fragment, C239 insertion mutant
6P6D: “Human IGG1 Fc fragment, C239 insertion mutant”. X-ray diffraction, 5 ligands (CYS, NAG, MAN), 2 pockets (best druggability 0.37). MolNFT v1 #159955 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P6D
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1 Fc fragment
- UniProt
- Q6MZV7
- Ligands
- CYS, NAG, MAN, BMA, FUC
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | IGG1 Fc fragment | protein | 208 | 11% helix, 47% strand | Q6MZV7 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B
- 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 | 114 | 0.37 | 0.74 | 23 | empty |
| 2 | 63 | 0.27 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1192 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6P6D · Human IGG1 Fc fragment, C239 insertion mutant · 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 Q6MZV7
- Elsewhere: RCSB PDB 6P6D · PDBe 6P6D · UniProt Q6MZV7
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