SMTL ID : 9kmc.1

Cryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2 and anti-CD25 Fab S417

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 14 residues within 4Å: Chain B: F.11, N.13, N.17, S.19, A.59, C.60, N.61, I.63, R.105, L.106, M.107, A.108, S.195, P.196 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.13 Hydrogen bonds: B:R.105, B:R.105, B:L.106, B:A.108, B:N.61 NAG-NAG-FUC.2: 8 residues within 4Å: Chain B: H.36, W.38, R.43, W.44, N.45, R.81, L.83, W.90 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 8 residues within 4Å: Chain B: V.115, N.123, S.125, E.165, W.166, C.168 Chain C: Y.167, T.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.166

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 6 residues within 4Å: Chain C: F.43, Y.47, N.49, L.84, Q.94, W.133 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: N.62, F.85, E.88, I.89, T.90 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.6: 5 residues within 4Å: Chain C: E.136, N.137, N.153, N.154, R.155 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.136, C:N.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Itoh-Nakadai, A. et al., CXCR4 induces memory formation over exhaustion in CAR-T cells to achieve durable leukemia targeting. To Be Published

Release Date

2025-11-19

Peptides

Interleukin-2 receptor subunit alpha: A
Interleukin-2 receptor subunit beta: B
Cytokine receptor common subunit gamma: C
Interleukin-2: D
Fab S417 heavy chain: E
Fab S417 light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Interleukin-2 receptor subunit alpha

Interleukin-2 receptor subunit beta

Cytokine receptor common subunit gamma

Interleukin-2

Fab S417 heavy chain

Fab S417 light chain

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