SMTL ID : 7a0v.1

Crystal structure of the 5-phosphatase domain of Synaptojanin1 in complex with a nanobody

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-3-3-mer

Ligands

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

PO4.1: 4 residues within 4Å: Chain A: R.289, W.291 Chain F: Y.59, K.64 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Water bridges: F:Y.59 Salt bridges: F:K.64, A:R.289 PO4.8: 4 residues within 4Å: Chain E: Y.260, K.261, R.276 Ligands: MG.10 3 PLIP interactions: 3 interactions with chain E Water bridges: E:E.67 Salt bridges: E:K.261, E:R.276 PO4.9: 4 residues within 4Å: Chain E: L.250, E.251, G.252, W.286 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.251

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.19, E.67, D.334 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.67, A:E.67, H2O.1 MG.7: 3 residues within 4Å: Chain C: N.19, E.67, D.334 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.67, H2O.9 MG.10: 2 residues within 4Å: Chain E: E.67 Ligands: PO4.8 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.67, H2O.10, H2O.11

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: P.190, M.191 Chain B: Q.1, V.2, G.26, S.27, T.28, R.32 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.27, B:S.27 Water bridges: B:T.28, B:R.32, B:R.32 GOL.4: 3 residues within 4Å: Chain A: R.25, S.80, T.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.80, A:T.82, A:T.82 GOL.5: 3 residues within 4Å: Chain A: N.99, K.100, R.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.119, A:R.119 Water bridges: A:K.100, A:K.100 GOL.6: 5 residues within 4Å: Chain A: Q.225, N.226, W.227, D.228, K.253 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.225, A:N.226, A:W.227, A:D.228, A:D.228, A:K.253

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

Synaptojanin-1: ACE
Nanobody 13015: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Synaptojanin-1

Nanobody 13015