SMTL ID : 5xwu.1

Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

hetero-2-2-mer

Ligands

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.1: 4 residues within 4Å: Chain A: A.284, N.285, I.300, Q.302 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: N.312, V.318 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain D: N.312, R.317, V.318, R.319 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: S.238, N.240 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.56 NAG.7: 1 residues within 4Å: Chain C: N.240 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.240 NAG.8: 4 residues within 4Å: Chain C: S.283, A.284, N.285, Q.302 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.302

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 6 residues within 4Å: Chain A: Q.53, R.54, E.56, R.69, Q.71, F.149 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.53, A:Q.53, A:E.56 MES.9: 7 residues within 4Å: Chain C: Q.53, R.54, E.56, R.69, Q.71, F.149 Chain D: H.179 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.53, C:Q.71 Salt bridges: D:H.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto-Ito, S. et al., Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation. Nat Commun (2018)

Release Date

2018-06-06

Peptides

Receptor-type tyrosine-protein phosphatase delta: AC
Leucine-rich repeat and fibronectin type III domain-containing protein 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Receptor-type tyrosine-protein phosphatase delta

Leucine-rich repeat and fibronectin type III domain-containing protein 1