Research workbench

Crystal structure of receptor-Fab complex

Analyse Crystal structure of receptor-Fab complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JZJ
Type: protein
Length: 1,368 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-3 receptor subunit alpha; Fab heavy chain; Fab light chain
UniProt: P26951
Ligands: NAG, FUL, BMA, MAN, FUC
Pockets: 16 · best druggability 0.62

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Interleukin-3 receptor subunit alpha	protein	250	3% helix, 52% strand	P26951
D	Interleukin-3 receptor subunit alpha	protein	251	4% helix, 49% strand	P26951
A	Fab heavy chain	protein	214	7% helix, 51% strand	—
B, L	Fab light chain	protein	219	5% helix, 50% strand	—
H	Fab heavy chain	protein	215	9% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, H, D, A
FUL · beta-L-fucopyranose · sugar · 5 copies · chains C, H, L, D, A
BMA · beta-D-mannopyranose · sugar · 2 copies · chains H, A
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains H
FUC · alpha-L-fucopyranose · sugar · chains D
GOL · Glycerol · additive · 2 copies · chains D, H, L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.62	0.76	52	empty
2	357	0.56	0.75	51	empty
3	61	0.53	0.88	20	empty
4	196	0.46	0.74	31	empty
5	182	0.46	0.75	27	empty

Interfaces

8 interfaces between chains.

A–B · 1752 Å² buried · 20 hydrogen bonds · protein-protein
H–L · 1707 Å² buried · 19 hydrogen bonds · protein-protein
C–H · 571 Å² buried · 5 hydrogen bonds · protein-protein
D–A · 566 Å² buried · 2 hydrogen bonds · protein-protein
C–L · 413 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

4JZJ · Crystal Structure of Receptor-Fab Complex · the same entry in another collection · chain L against L, TM-score 1.00
P26951 · AlphaFold monomer V2.0 prediction for interleukin-3 receptor subunit alpha (P26951) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P26951
Elsewhere: RCSB PDB 4JZJ · PDBe 4JZJ · UniProt P26951

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