SMTL ID : 4yh6.1

Crystal structure of IL1RAPL1 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 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.1: 6 residues within 4Å: Chain A: A.59, L.61, N.111, T.113, Y.114 Chain B: E.280 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.59 NAG-NAG-BMA.4: 3 residues within 4Å: Chain B: N.127, L.131, R.215 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.2: 9 residues within 4Å: Chain A: Y.133, S.135, K.138, E.173, I.200, G.201, N.202 Chain B: L.98, Q.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.100 NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain A: N.253, T.255, R.293, L.295, S.305, S.307, I.309 Chain B: D.81 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.293, A:S.305, A:L.295 NAG-NAG-BMA-MAN-MAN.5: 8 residues within 4Å: Chain A: L.98, Q.100 Chain B: Y.133, S.135, K.138, E.173, G.201, N.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.100

1 x NAG- NAG- BMA- MAN: 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.6: 6 residues within 4Å: Chain A: D.81 Chain B: N.253, T.255, R.293, S.307, I.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.81

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

NAG.7: 3 residues within 4Å: Chain A: N.127, C.132, R.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.215, A:R.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamagata, A. et al., Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation. Nat Commun (2015)

Release Date

2015-05-06

Peptides

Interleukin-1 receptor accessory protein-like 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Interleukin-1 receptor accessory protein-like 1

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