SMTL ID : 3mtc.1 (1 other biounit)

Crystal Structure of INPP5B in complex with phosphatidylinositol 4-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.4, Q.6, F.8, H.100, Y.103, H.133, V.305 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.4, A:Y.4, A:Q.6, A:H.100 GOL.5: 4 residues within 4Å: Chain A: G.115, I.116, M.117, R.153 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.117, A:R.153, A:R.153 Water bridges: A:G.115, A:N.122

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.18, E.46 Ligands: PIF.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.46, H2O.3, H2O.3, H2O.3

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

PIF.3: 15 residues within 4Å: Chain A: E.46, L.49, K.51, F.54, I.116, N.122, K.123, H.143, A.146, H.147, Y.245, K.246, K.259, R.261 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:K.51, A:I.116, A:I.116 Hydrogen bonds: A:E.46, A:N.122, A:K.123, A:K.123, A:H.147, A:Y.245 Water bridges: A:E.46, A:H.147, A:R.194, A:K.246, A:D.291, A:D.291 Salt bridges: A:K.123, A:K.246, A:K.259, A:R.261

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

SO4.4: 3 residues within 4Å: Chain A: S.50, K.51, E.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51, A:E.52 Salt bridges: A:K.51

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

CL.6: 3 residues within 4Å: Chain A: H.284, M.285, A.286 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tresaugues, L. et al., Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases. Structure (2014)

Release Date

2010-06-30

Peptides

Type II inositol-1,4,5-trisphosphate 5-phosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Type II inositol-1,4,5-trisphosphate 5-phosphatase

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