SMTL ID : 5wy8.1

Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.07 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 2 residues within 4Å: Chain A: S.232, N.234 No protein-ligand interaction detected (PLIP)

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 B: N.238, T.240, R.278, L.280, S.290, I.294 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.280 Hydrogen bonds: B:S.290 NAG-NAG.3: 4 residues within 4Å: Chain B: L.46, N.96, T.98, Y.99 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: Y.118, S.120, K.123, E.158, I.185, G.186, N.187 No protein-ligand interaction detected (PLIP)

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.4: 5 residues within 4Å: Chain B: V.19, N.112, L.116, C.117, R.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.200

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

NAG.6: 2 residues within 4Å: Chain A: S.277, N.279 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.37, L.40 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.40

3 x ZN: ZINC ION(Non-covalent)

ZN.8: 1 residues within 4Å: Chain B: H.318 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.318 ZN.9: 1 residues within 4Å: Chain B: D.183 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.183 ZN.10: 2 residues within 4Å: Chain B: E.182, H.283 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.182, B:E.182, B:H.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Won, S.Y. et al., LAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate. Front Mol Neurosci (2017)

Release Date

2017-11-22

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