MolNFT v1 · #187138 · protein

Nanobody bound to interleukin-2RBETA

7S2S · IL2RB-binding nanobody: “Nanobody bound to interleukin-2RBETA”. X-ray diffraction, 4 ligands (NAG, FUC, BMA), 3 pockets (best druggability 0.40). MolNFT v1 #187138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7S2S
Type: protein
Length: 657 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IL2RB-binding nanobody; Interleukin-2 receptor subunit beta
UniProt: P14784
Ligands: NAG, FUC, BMA, SO4
Pockets: 3 · best druggability 0.40

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	IL2RB-binding nanobody	protein	127	15% helix, 43% strand	—
B	Interleukin-2 receptor subunit beta	protein	199	4% helix, 49% strand	P14784
A	IL2RB-binding nanobody	protein	127	15% helix, 41% strand	—
D	Interleukin-2 receptor subunit beta	protein	204	3% helix, 48% strand	P14784

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains B, D, A
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains B, D
BMA · beta-D-mannopyranose · sugar · 2 copies · chains D
SO4 · Sulfate ion · ion · 13 copies · chains B, D, A

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

Pockets

3 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	128	0.40	0.75	21	empty
2	59	0.28	0.74	13	empty
3	51	0.27	0.74	11	empty

Interfaces

4 interfaces between chains.

A–D · 690 Å² buried · 10 hydrogen bonds · protein-protein
C–B · 667 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 429 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 89 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 6 glycan, 6 modified (disulfide, N-glycosylation, methylation).

Compared structures

7S2S · nanobody bound to Interleukin-2Rbeta · the same entry in another collection · chain C against C, TM-score 1.00
P14784 · AlphaFold monomer V2.0 prediction for interleukin-2 receptor subunit beta (P14784) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P14784
Elsewhere: RCSB PDB 7S2S · PDBe 7S2S · UniProt P14784

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