SMTL ID : 7s2r.1

nanobody bound to IL-2Rg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG.1: 6 residues within 4Å: Chain A: F.14, Y.18, N.20, H.53, L.55, Q.65 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.65

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

NAG.2: 4 residues within 4Å: Chain A: P.31, N.33, F.56, E.59 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.59 NAG.3: 5 residues within 4Å: Chain A: E.107, N.108, N.124, R.126 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.126 Hydrogen bonds: A:E.107, A:N.124

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

SO4.4: 3 residues within 4Å: Chain A: P.192, I.193, H.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.194, A:H.194 Salt bridges: A:H.194 SO4.5: 3 residues within 4Å: Chain A: K.68 Chain B: R.104, W.106 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.121 Salt bridges: A:K.68 SO4.6: 3 residues within 4Å: Chain A: K.41, N.42, S.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.42, A:S.43 SO4.7: 5 residues within 4Å: Chain A: P.106, E.107, N.108, L.109, H.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.106, A:N.108, A:L.109 Salt bridges: A:H.191 SO4.12: 5 residues within 4Å: Chain A: S.43, N.45, H.72 Chain B: Y.32, R.54 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.43, A:N.45, A:N.45 Salt bridges: A:H.72, B:R.54 SO4.13: 2 residues within 4Å: Chain A: N.108 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.108 SO4.14: 4 residues within 4Å: Chain B: Y.33, Y.52, R.62, Q.111 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.33, B:Q.111 Salt bridges: B:R.62 SO4.15: 1 residues within 4Å: Chain B: R.43 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.43

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: F.12, H.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.185 GOL.9: 4 residues within 4Å: Chain A: R.173, Q.184, H.185, W.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:W.186, A:W.186 GOL.10: 3 residues within 4Å: Chain A: K.96, N.99, S.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.96, A:N.99, A:S.182, A:S.182 GOL.11: 2 residues within 4Å: Chain A: R.171, W.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.171, A:R.171, A:W.189 GOL.16: 6 residues within 4Å: Chain B: G.47, S.64, S.65, L.112, G.113, G.114 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.47, B:S.65, B:S.65, B:G.114 Water bridges: B:R.116 GOL.17: 2 residues within 4Å: Chain A: H.130 Chain B: R.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.116

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

Cytokine receptor common subunit gamma: A
nanobody gamma-nb6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytokine receptor common subunit gamma

nanobody gamma-nb6