MolNFT v1 · #50387 · protein

Fc-fragment of monoclonal antibody IGG2B from mus musculus

2RGS · Ig gamma-2B heavy chain: “Fc-fragment of monoclonal antibody IGG2B from mus musculus”. X-ray diffraction, 4 ligands (NAG, MAN, GAL), 4 pockets (best druggability 0.41). MolNFT v1 #50387 on GenesisL1: 3D structure, binding sites and…

PDB: 2RGS
Type: protein
Length: 413 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig gamma-2B heavy chain
UniProt: P01867
Ligands: NAG, MAN, GAL, FUC
Pockets: 4 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig gamma-2B heavy chain	protein	206	11% helix, 51% strand	P01867
B	Ig gamma-2B heavy chain	protein	207	11% helix, 51% strand	P01867

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 6 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

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	92	0.41	0.79	20	empty
2	94	0.41	0.78	20	empty
3	70	0.35	0.76	20	empty
4	66	0.34	0.76	14	empty

Interfaces

1 interface between chains.

A–B · 1077 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2RGS · FC-fragment of monoclonal antibody IGG2B from Mus musculus · the same entry in another collection · chain A against A, TM-score 1.00
P01867 · AlphaFold monomer V2.0 prediction for ig gamma-2B chain C region (P01867) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P01867
Elsewhere: RCSB PDB 2RGS · PDBe 2RGS · UniProt P01867

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