SMTL ID : 5xnp.1

Crystal structures of human SALM5 in complex with human PTPdelta

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.73 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.60 NAG.2: 4 residues within 4Å: Chain A: K.296, Y.324, N.326, T.328 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.296 Hydrogen bonds: A:N.326, A:T.328 NAG.3: 4 residues within 4Å: Chain A: N.317, V.323, Y.324, D.325 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.317 NAG.16: 1 residues within 4Å: Chain B: N.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.60 NAG.17: 3 residues within 4Å: Chain B: N.317, V.323, D.325 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.317 NAG.18: 3 residues within 4Å: Chain B: Y.324, N.326, T.328 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.326 NAG.31: 3 residues within 4Å: Chain C: S.268, N.270, Q.287 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.268, C:Q.287, C:T.289 NAG.35: 3 residues within 4Å: Chain D: N.270, Q.287, T.289 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.289

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: N.48, R.71, N.72 Chain B: H.167 Ligands: CL.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.72 NA.19: 4 residues within 4Å: Chain A: H.167 Chain B: F.49, R.71 Ligands: CL.28 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.191, B:R.71

12 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: N.192, K.193 Chain B: T.51, T.73 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: S.126, S.127 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: H.80, D.104 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain A: P.4, D.37, R.39 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.37 CA.9: 2 residues within 4Å: Chain A: H.113, E.137 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.137, H2O.1 CA.10: 2 residues within 4Å: Chain A: A.353, T.354 No protein-ligand interaction detected (PLIP) CA.20: 5 residues within 4Å: Chain A: F.49, T.51 Chain B: N.192, K.193, G.226 No protein-ligand interaction detected (PLIP) CA.21: 1 residues within 4Å: Chain B: S.127 No protein-ligand interaction detected (PLIP) CA.22: 2 residues within 4Å: Chain B: H.80, D.104 No protein-ligand interaction detected (PLIP) CA.23: 2 residues within 4Å: Chain B: P.4, D.37 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.37 CA.24: 2 residues within 4Å: Chain B: H.113, E.137 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.113, H2O.2, H2O.3 CA.25: 2 residues within 4Å: Chain B: A.353, T.354 No protein-ligand interaction detected (PLIP)

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 2 residues within 4Å: Chain A: N.52, K.54 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: K.26, D.47 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: N.72, R.97 Chain B: H.167 Ligands: NA.4 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain B: N.52, K.54 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain B: K.26, D.47 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: H.167 Chain B: N.72 Ligands: NA.19 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain C: N.46, R.71 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain C: E.1, N.83 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain C: R.121, R.204 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain D: N.46, R.71 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain D: E.1, N.83 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain D: R.121, R.204 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 4 residues within 4Å: Chain A: S.70, R.71, H.92, N.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.70, A:N.94 Salt bridges: A:R.71, A:H.92 SO4.15: 2 residues within 4Å: Chain A: H.279 Chain C: K.239 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:K.239, A:H.279 Hydrogen bonds: A:H.281 SO4.29: 4 residues within 4Å: Chain B: S.70, R.71, H.92, N.94 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.70, B:N.94 Salt bridges: B:R.71, B:H.92 SO4.30: 3 residues within 4Å: Chain B: H.279, H.281 Chain D: E.283 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.281 Salt bridges: B:H.279, D:K.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, Z. et al., Structural basis of SALM5-induced PTP delta dimerization for synaptic differentiation. Nat Commun (2018)

Release Date

2018-01-24

Peptides

Leucine-rich repeat and fibronectin type-III domain-containing protein 5: AB
Receptor-type tyrosine-protein phosphatase delta: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

Leucine-rich repeat and fibronectin type-III domain-containing protein 5

Receptor-type tyrosine-protein phosphatase delta