MolNFT v1 · #117054 · protein

Beta common receptor in complex with a Fab

5DWU · Cytokine receptor common subunit beta: “Beta common receptor in complex with a Fab”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.73). MolNFT v1 #117054 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5DWU
Type: protein
Length: 748 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytokine receptor common subunit beta; Fab - heavy chain; Fab - light chain
UniProt: P32927
Ligands: NAG
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytokine receptor common subunit beta	protein	161	9% helix, 19% strand	P32927
B	Cytokine receptor common subunit beta	protein	181	0% helix, 44% strand	P32927
H	Fab - heavy chain	protein	199	3% helix, 36% strand	—
L	Fab - light chain	protein	207	5% helix, 38% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.73	0.93	24	empty
2	87	0.71	0.94	24	empty
3	377	0.66	0.80	35	empty
4	121	0.66	0.88	31	empty
5	227	0.57	0.79	35	empty

Interfaces

6 interfaces between chains.

A–B · 1581 Å² buried · 11 hydrogen bonds · protein-protein
H–L · 1429 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 440 Å² buried · 8 hydrogen bonds · protein-protein
B–H · 280 Å² buried · 6 hydrogen bonds · protein-protein
B–L · 177 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5DWU · Beta common receptor in complex with a Fab · the same entry in another collection · chain A against A, TM-score 1.00
P32927 · AlphaFold monomer V2.0 prediction for cytokine receptor common subunit beta (P32927) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P32927
Elsewhere: RCSB PDB 5DWU · PDBe 5DWU · UniProt P32927

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