SMTL ID : 3wo3.1 (5 other biounits)

Crystal structure of IL-18 in complex with IL-18 receptor alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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(Non-functional Binders)

NAG-NAG-FUC.1: 3 residues within 4Å: Chain B: N.133, H.173, G.176 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.176 NAG-NAG-FUC.5: 9 residues within 4Å: Chain A: Q.56, P.57 Chain B: M.233, F.234, G.235, L.278, N.280, T.291 Ligands: SO4.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:P.57 Hydrophobic interactions: B:T.291

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

NAG-NAG-BMA-MAN-MAN-MAN.2: 7 residues within 4Å: Chain B: G.16, R.97, K.99, H.100, V.169, F.171, N.180 No protein-ligand interaction detected (PLIP)

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.3: 6 residues within 4Å: Chain B: V.108, S.110, I.112, Y.165, N.186, T.188 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(Post Translational Modification)

NAG-NAG-BMA.4: 3 residues within 4Å: Chain B: V.208, R.217, N.219 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.217

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

SO4.6: 5 residues within 4Å: Chain A: H.109, D.110, N.111, K.112 Chain B: K.117 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.111, A:N.111, A:K.112 Salt bridges: A:H.109, A:K.112, B:K.117 SO4.7: 4 residues within 4Å: Chain A: D.35, C.38, R.39, Q.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.154, A:Q.154 Salt bridges: A:R.39 SO4.10: 8 residues within 4Å: Chain A: Y.1, S.55 Chain B: M.233, G.235, E.236, E.237 Ligands: NAG-NAG-FUC.5, SO4.12 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:S.55, B:G.235, B:E.236, B:E.237, B:E.237, B:E.237 SO4.11: 4 residues within 4Å: Chain B: P.242, N.243, H.245, E.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.242, B:N.243 Salt bridges: B:H.245 SO4.12: 6 residues within 4Å: Chain B: G.235, E.236, E.237, N.238, G.239 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.237, B:N.238, B:N.238, B:G.239 SO4.13: 4 residues within 4Å: Chain B: S.56, S.57, R.58 Ligands: NAG.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.57, B:S.57 Salt bridges: B:R.58 SO4.14: 2 residues within 4Å: Chain B: E.147, N.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.149

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

NAG.8: 3 residues within 4Å: Chain B: E.72, N.74 Ligands: SO4.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.74 NAG.9: 1 residues within 4Å: Chain B: N.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutsumi, N. et al., The structural basis for receptor recognition of human interleukin-18. Nat Commun (2014)

Release Date

2014-12-17

Peptides

Interleukin-18: A
Interleukin-18 receptor 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Interleukin-18

Interleukin-18 receptor 1

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