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Structure of an avian igy-Fc 3-4 fragment

Analyse Structure of an avian igy-Fc 3-4 fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2W59
Type: protein
Length: 429 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Igy FCU3-4
Ligands: NAG, MAN
Pockets: 4 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Igy FCU3-4	protein	215	11% helix, 44% strand	—
B	Igy FCU3-4	protein	214	11% helix, 44% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.36	0.78	17	GOL
2	53	0.31	0.76	12	empty
3	61	0.28	0.73	12	empty
4	57	0.25	0.72	14	empty

Interfaces

1 interface between chains.

A–B · 1420 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2W59 · Structure of an avian igy-Fc 3-4 fragment · 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
Elsewhere: RCSB PDB 2W59 · PDBe 2W59

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