MolNFT v1 · #10107 · protein

Structure of immunoglobulin

1IGT · IGG2A intact antibody - MAB231: “Structure of immunoglobulin”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 13 pockets (best druggability 0.59). MolNFT v1 #10107 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1IGT
Type: protein
Length: 1,316 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG2A intact antibody - MAB231
UniProt: P01863
Ligands: NAG, MAN, BMA, GAL, FUL, FUC
Pockets: 13 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	IGG2A intact antibody - MAB231	protein	214	7% helix, 49% strand	—
B, D	IGG2A intact antibody - MAB231	protein	444	7% helix, 47% strand	P01863

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, D
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, D
BMA · beta-D-mannopyranose · sugar · 2 copies · chains B, D
GAL · beta-D-galactopyranose · sugar · 2 copies · chains B, D
FUL · beta-L-fucopyranose · sugar · chains B
FUC · alpha-L-fucopyranose · sugar · chains D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	490	0.59	0.74	60	empty
2	156	0.50	0.78	25	empty
3	212	0.46	0.74	29	empty
4	68	0.46	0.82	19	empty
5	100	0.43	0.78	27	empty

Interfaces

3 interfaces between chains.

A–B · 2208 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 2073 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1473 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1IGT · Structure of immunoglobulin · the same entry in another collection · chain A against A, TM-score 1.00
P01863 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, a allele (P01863) · a predicted model of the same protein · chain B against A, TM-score 0.52

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 P01863
Elsewhere: RCSB PDB 1IGT · PDBe 1IGT · UniProt P01863

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