SMTL ID : 5mzv.1

IL-23:IL-23R:Nb22E11 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 12 residues within 4Å: Chain A: I.23, W.24, E.25, V.32, E.34, H.105, W.112, K.157, M.211, D.213, Y.220, N.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.112 Hydrogen bonds: A:E.34

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

NAG-NAG.2: 6 residues within 4Å: Chain C: G.45, M.46, N.47, W.88, K.90, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain C: Y.138, S.139, G.140, N.141, N.180 Ligands: NAG-NAG.5, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain C: S.139, Y.178, I.179, N.180 Ligands: NAG-NAG.4, NAG-NAG.4 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: 9 residues within 4Å: Chain C: H.33, W.35, Y.51, Q.53, I.80, N.81, K.82, T.83, T.84 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.53

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: K.118, T.147, N.184 Chain D: F.51, S.52, W.53 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain C: D.126, D.129, N.147, G.149 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain C: N.47, I.48, S.49, W.88 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Chain A: D.84 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.81, A:E.81, A:D.84, A:D.84

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

NAG.10: 3 residues within 4Å: Chain C: N.262, T.264, N.266 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.264, C:N.266 NAG.11: 3 residues within 4Å: Chain C: N.273, T.275, Y.276 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bloch, Y. et al., Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12R beta 1. Immunity (2018)

Release Date

2018-01-03

Peptides

Interleukin-12 subunit beta: A
Interleukin-23 subunit alpha: B
Interleukin-23 receptor: C
Nanobody 22E11: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Interleukin-12 subunit beta

Interleukin-23 subunit alpha

Interleukin-23 receptor

Nanobody 22E11

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