Research workbench

Glycosylated KNOB/DUMMY-HOLE/DUMMY Fc fragment

Analyse Glycosylated KNOB/DUMMY-HOLE/DUMMY Fc fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YTB
Type: protein
Length: 416 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.65
Source: Homo sapiens
Molecule: Immunoglobulin gamma-1 heavy chain
UniProt: P0DOX5
Ligands: NAG, MAN, BMA, GAL, FUC
Pockets: 3 · best druggability 0.37

Structure

x-ray diffraction · resolution 1.65 · 2 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Immunoglobulin gamma-1 heavy chain	protein	207	11% helix, 48% strand	P0DOX5
B	Immunoglobulin gamma-1 heavy chain	protein	209	10% helix, 47% strand	P0DOX5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.37	0.77	18	empty
2	80	0.31	0.73	20	empty
3	55	0.29	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 1137 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6YTB · Glycosylated KNOB/DUMMY-HOLE/DUMMY Fc fragment · the same entry in another collection · chain A against A, TM-score 1.00
P0DOX5 · AlphaFold monomer V2.0 prediction for immunoglobulin gamma-1 heavy chain (P0DOX5) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P0DOX5
Elsewhere: RCSB PDB 6YTB · PDBe 6YTB · UniProt P0DOX5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.