SMTL ID : 5xwt.1

Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.18 Å

Oligo State

hetero-2-2-mer

Ligands

5 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: 3 residues within 4Å: Chain A: A.284, N.285, Q.302 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain B: A.55, N.56 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: S.238, N.240, L.277 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: R.286, L.318, D.321, N.322 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.286, D:R.286 NAG-NAG.6: 1 residues within 4Å: Chain D: N.313 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.3: 2 residues within 4Å: Chain C: N.285, Q.302 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.240 NAG.8: 1 residues within 4Å: Chain B: N.313 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain B: L.318, N.322 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.318 Hydrogen bonds: B:N.322 NAG.10: 1 residues within 4Å: Chain D: N.56 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.56

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 5: 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 5

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