SMTL ID : 5xnq.1

Crystal structures of human SALM5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: R.38, K.56, A.59, N.60 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.59 Hydrogen bonds: A:N.60 NAG.12: 4 residues within 4Å: Chain B: R.38, K.56, A.59, N.60 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.59 Hydrogen bonds: B:N.60

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

NA.2: 6 residues within 4Å: Chain A: Q.195, P.228, L.229, H.230, A.251, S.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.228, A:S.252 NA.3: 3 residues within 4Å: Chain A: N.48, F.49, R.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.48 NA.4: 3 residues within 4Å: Chain A: S.95, N.119 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 NA.13: 6 residues within 4Å: Chain B: Q.195, P.228, L.229, H.230, A.251, S.252 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.252, B:S.252 NA.14: 3 residues within 4Å: Chain B: N.48, F.49, R.71 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.48 Water bridges: B:D.47, B:D.47 NA.15: 3 residues within 4Å: Chain B: S.95, N.119 Ligands: CL.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.119

8 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.5: 4 residues within 4Å: Chain A: N.192, K.193, G.226 Chain B: T.73 No protein-ligand interaction detected (PLIP) CA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: R.89, H.114 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain A: H.180, H.182 No protein-ligand interaction detected (PLIP) CA.16: 4 residues within 4Å: Chain A: T.73 Chain B: N.192, K.193, G.226 No protein-ligand interaction detected (PLIP) CA.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain B: R.89, H.114 No protein-ligand interaction detected (PLIP) CA.19: 2 residues within 4Å: Chain B: H.180, H.182 No protein-ligand interaction detected (PLIP)

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

CL.9: 1 residues within 4Å: Chain B: Y.143 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: T.73 Ligands: NA.4 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain A: Y.143 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: T.73 Ligands: NA.15 Ligand excluded by PLIP

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

SO4.11: 3 residues within 4Å: Chain A: S.70, R.71, N.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.70, A:N.94 Water bridges: A:H.92 Salt bridges: A:R.71 SO4.22: 3 residues within 4Å: Chain B: S.70, R.71, N.94 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.70, B:N.94 Water bridges: B:T.68, B:H.92 Salt bridges: B:R.71

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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