SMTL ID : 9eth.1

Complex structure of IL-36R D1-D2 domain with 36R-P192 and BI655130 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-1-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: 4 residues within 4Å: Chain D: M.8, K.9, V.73, N.90 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.6 Hydrogen bonds: D:F.7

1 x NAG- NAG- BMA- MAN- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-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

NAG-NAG-BMA-MAN-NAG-MAN.2: 12 residues within 4Å: Chain C: W.7 Chain D: N.22, C.23, T.24, T.29, S.30, G.31, E.32, V.33, V.35, T.59 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.31, D:E.32

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

SO4.3: 4 residues within 4Å: Chain A: K.67, R.85, R.87 Ligands: NA.6 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.67, A:R.87 SO4.4: 4 residues within 4Å: Chain A: Y.27, S.28 Chain D: E.169, R.171 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.28 Water bridges: D:R.171, D:R.171 Salt bridges: D:R.171 SO4.5: 2 residues within 4Å: Chain A: T.199, R.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.199 Salt bridges: A:R.216 SO4.7: 3 residues within 4Å: Chain B: P.8, G.9, T.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.9, B:T.10 SO4.8: 3 residues within 4Å: Chain B: K.40, Q.43, R.46 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.38, B:Q.43 Salt bridges: B:K.40, B:R.46 SO4.9: 4 residues within 4Å: Chain A: Q.111 Chain B: G.42, Q.43, A.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.44 Water bridges: B:Q.43, B:A.44 SO4.10: 3 residues within 4Å: Chain B: P.60, D.61, R.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.61, B:D.61, B:R.62, B:R.78 Salt bridges: B:R.62 SO4.12: 3 residues within 4Å: Chain D: G.2, C.3, R.86 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.2, D:C.3 Salt bridges: D:R.86

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

NA.6: 3 residues within 4Å: Chain A: K.67, R.87 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.67, A:R.87

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

NAG.11: 1 residues within 4Å: Chain D: N.165 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.165

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 6 residues within 4Å: Chain D: E.58, T.59, W.60, P.132, K.133 Ligands: NAG-NAG-BMA-MAN-NAG-MAN.2 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.59, D:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Velcicky, J. et al., Discovery of selective low molecular weight interleukin-36 receptor antagonists by encoded library technologies. Nat Commun (2025)

Release Date

2025-02-26

Peptides

BI00655130 Fab heavy chain: A
BI00655130 Fab light chain: B
ACE-PHE-VAL-GLU-5CW-3PN-TRP-ASP-TYR-VAL-CHG-6G5-SER-GLU-CYS-NH2: C
Interleukin-1 receptor-like 2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

D
R

BI00655130 Fab heavy chain

BI00655130 Fab light chain

ACE-PHE-VAL-GLU-5CW-3PN-TRP-ASP-TYR-VAL-CHG-6G5-SER-GLU-CYS-NH2

Interleukin-1 receptor-like 2

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