SMTL ID : 7a17.2 (2 other biounits)

Crystal structure of the 5-phosphatase domain of Synaptojanin1 bound to its substrate diC8-PI(3,4,5)P3 in complex with a nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

hetero-1-1-mer

Ligands

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: A.164, R.206, Y.256, R.272 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.206, A:Y.256 Salt bridges: A:R.272 PO4.2: 11 residues within 4Å: Chain A: N.13, E.63, H.161, A.164, D.202, N.204, R.206, Y.256, H.331 Ligands: PO4.1, MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.13, A:E.63, A:E.63, A:N.204, A:N.204, A:R.206, A:Y.256 Salt bridges: A:K.141, A:H.161 PO4.3: 3 residues within 4Å: Chain A: L.67, N.140, K.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.140 Salt bridges: A:K.141

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: N.15, E.63 Ligands: PO4.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.63, A:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Paesmans, J. et al., A structure of substrate-bound Synaptojanin1 provides new insights in its mechanism and the effect of disease mutations. Elife (2020)

Release Date

2020-12-30

Peptides

Isoform 2 of Synaptojanin-1: A
Nanobody 13015: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isoform 2 of Synaptojanin-1

Nanobody 13015

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