SMTL ID : 4yh7.1

Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.40 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 B: Y.133, S.135, K.138, E.173, N.202, E.219 No protein-ligand interaction detected (PLIP)

1 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: 8 residues within 4Å: Chain B: N.253, T.255, R.257, R.293, L.295, S.305, S.307, I.309 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.295 Hydrogen bonds: B:R.293, B:S.305, B:L.295

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

NAG.3: 5 residues within 4Å: Chain B: A.59, L.61, N.111, T.113, Y.114 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.59, B:L.61 NAG.4: 5 residues within 4Å: Chain B: N.127, D.128, T.129, G.130, L.131 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.130, B:L.131, B: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

Receptor-type tyrosine-protein phosphatase delta: A
Interleukin-1 receptor accessory protein-like 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Receptor-type tyrosine-protein phosphatase delta

Interleukin-1 receptor accessory protein-like 1

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