MolNFT v1 · #104318 · protein

Crystal structure of a chemoenzymatic glycoengineered disialylated Fc (di-sfc)

4Q6Y · Ig gamma-1 chain C region: “Crystal structure of a chemoenzymatic glycoengineered disialylated Fc (di-sfc)”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.59). MolNFT v1 #104318 on GenesisL1: 3D…

PDB: 4Q6Y
Type: protein
Length: 808 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, SIA
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig gamma-1 chain C region	protein	208	11% helix, 44% strand	P01857
B	Ig gamma-1 chain C region	protein	206	11% helix, 46% strand	P01857
C	Ig gamma-1 chain C region	protein	199	11% helix, 46% strand	P01857
D	Ig gamma-1 chain C region	protein	195	11% helix, 45% 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 · 3 copies · chains B, C, D
SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	341	0.59	0.77	27	empty
2	284	0.57	0.77	44	empty
3	53	0.39	0.81	11	empty
4	65	0.31	0.75	16	empty
5	64	0.30	0.75	16	empty

Interfaces

4 interfaces between chains.

A–B · 1141 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1125 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 244 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 137 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4Q6Y · Crystal structure of a chemoenzymatic glycoengineered disialylated Fc (di-sFc) · 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 4Q6Y · PDBe 4Q6Y · UniProt P01857

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