SMTL ID : 5rx0.1

INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z57258487

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x NVD: N-{[4-(dimethylamino)phenyl]methyl}-4H-1,2,4-triazol-4-amine(Non-covalent)

NVD.1: 6 residues within 4Å: Chain A: Y.47, Q.76, E.77, I.78, T.79, S.80 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.47 pi-Stacking: A:Y.47

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 7 residues within 4Å: Chain A: G.138, T.139, T.186, T.319, D.405, Q.406, H.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.319 Water bridges: A:T.139 DMS.3: 6 residues within 4Å: Chain A: L.176, Y.286, S.360, S.361, H.407, L.409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.361 DMS.4: 6 residues within 4Å: Chain A: H.183, H.238, K.284, C.425, T.441, P.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.284, A:C.425

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

PO4.5: 10 residues within 4Å: Chain A: N.18, E.59, H.147, S.150, D.193, N.195, R.197, Y.250, H.307 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.18, A:S.150, A:D.193, A:N.195, A:R.197, A:Y.250 Water bridges: A:R.197, A:Y.250 Salt bridges: A:H.147, A:H.307

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: N.18, E.59 Ligands: PO4.5 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.59, H2O.2, H2O.4, H2O.7, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, W.J. et al., Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2. Structure (2024)

Release Date

2020-11-11

Peptides

Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1

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