SMTL ID : 7s2s.1 (1 other biounit)

nanobody bound to Interleukin-2Rbeta

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-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: 11 residues within 4Å: Chain B: F.11, N.17, S.19, N.61, I.63, R.105, L.106, M.107, A.108, Q.130, P.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.19, B:R.105, B:L.106, B:A.108, B:N.61 NAG-NAG-FUC.2: 7 residues within 4Å: Chain B: H.36, W.38, R.43, W.44, N.45, R.81, L.83 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.83

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: 3 residues within 4Å: Chain B: V.115, N.123, W.166 No protein-ligand interaction detected (PLIP)

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain B: R.42, R.43, W.44, K.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.43 Salt bridges: B:R.42, B:R.43 SO4.5: 3 residues within 4Å: Chain B: R.15, S.132, H.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.133 Water bridges: B:R.15 Salt bridges: B:R.15, B:H.133 SO4.6: 3 residues within 4Å: Chain B: Y.134, R.137, H.138 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.137, B:H.138 SO4.7: 2 residues within 4Å: Chain B: S.54, Q.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, M. et al., Facile discovery of surrogate cytokine agonists. Cell (2022)

Release Date

2022-03-30

Peptides

IL2Rb-binding nanobody: A
Interleukin-2 receptor subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

IL2Rb-binding nanobody

Interleukin-2 receptor subunit beta

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