SMTL ID : 7a17.1 (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

1 x IP9: (2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate(Non-covalent)

IP9.1: 20 residues within 4Å: Chain A: N.14, E.64, L.68, A.70, I.73, M.135, T.139, N.141, K.142, H.162, A.165, D.203, N.205, R.207, Y.257, K.258, K.271, R.273, H.332 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:A.70, A:I.73, A:T.139 Hydrogen bonds: A:N.14, A:E.64, A:N.141, A:K.142, A:K.142, A:N.205, A:R.207, A:Y.257, A:H.332 Salt bridges: A:K.142, A:H.162, A:K.258, A:K.271, A:R.273

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.16, E.64, D.331 Ligands: IP9.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.64, H2O.1, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.190, S.194, R.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.190, A:R.190, A:S.194, A:R.286, A:R.286 GOL.4: 3 residues within 4Å: Chain A: R.22, S.77, T.79 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.22, A:R.22, A:S.77, A:T.79, A:T.79

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
A

B
B

Isoform 2 of Synaptojanin-1

Nanobody 13015