MolNFT v1 · #138001 · protein

Crystal structure of human IGG4-SIGMA2 Fc fragment

5W5N · Immunoglobulin heavy constant gamma 4: “Crystal structure of human IGG4-SIGMA2 Fc fragment”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 2 pockets (best druggability 0.40). MolNFT v1 #138001 on GenesisL1: 3D structure, binding…

PDB: 5W5N
Type: protein
Length: 417 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: 2 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Immunoglobulin heavy constant gamma 4	protein	206	11% helix, 49% strand	P01861
B	Immunoglobulin heavy constant gamma 4	protein	211	12% helix, 48% 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 · chains 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

2 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	73	0.40	0.79	17	empty
2	56	0.28	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 1085 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5W5N · Crystal structure of human IgG4-Sigma2 Fc fragment · the same entry in another collection · chain A against A, TM-score 1.00
P01861 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 4 (P01861) · 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 P01861
Elsewhere: RCSB PDB 5W5N · PDBe 5W5N · UniProt P01861

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