SMTL ID : 4cml.1

Crystal Structure of INPP5B in complex with Phosphatidylinositol 3,4- bisphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x 52N: 1,2-dioctanoyl phosphatidyl epi-inositol (3,4)-bisphosphate(Non-covalent)

52N.1: 16 residues within 4Å: Chain A: E.46, L.49, K.51, F.54, I.116, M.117, N.122, K.123, A.146, H.147, Y.245, K.246, K.259, R.261 Ligands: 52N.6, 52N.11 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:K.51, A:F.54, A:F.54, A:I.116 Hydrogen bonds: A:N.122, A:K.123, A:K.123, A:Y.245, A:Y.245, A:R.261 Water bridges: A:N.16, A:N.192, A:N.192, A:R.194 Salt bridges: A:K.123, A:H.147, A:H.147, A:K.246, A:K.259, A:K.259, A:R.261 52N.6: 16 residues within 4Å: Chain B: E.46, L.49, K.51, F.54, I.116, M.117, N.122, K.123, A.146, H.147, Y.245, K.246, K.259, R.261 Ligands: 52N.1, 52N.11 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:K.51, B:F.54, B:F.54, B:I.116 Hydrogen bonds: B:N.122, B:K.123, B:K.123, B:Y.245, B:R.261 Water bridges: B:N.16, B:N.192, B:N.192, B:R.194 Salt bridges: B:K.123, B:H.147, B:H.147, B:K.246, B:K.259, B:K.259, B:R.261 52N.11: 16 residues within 4Å: Chain C: E.46, L.49, K.51, F.54, I.116, M.117, N.122, K.123, A.146, H.147, Y.245, K.246, K.259, R.261 Ligands: 52N.1, 52N.6 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:K.51, C:F.54, C:F.54, C:I.116 Hydrogen bonds: C:N.122, C:K.123, C:K.123, C:Y.245, C:Y.245, C:R.261 Water bridges: C:N.16, C:H.147, C:N.192, C:N.192 Salt bridges: C:K.123, C:H.147, C:H.147, C:K.246, C:K.259, C:K.259, C:R.261

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.18, E.46, D.291 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.46, H2O.1, H2O.1, H2O.1, H2O.2 MG.7: 3 residues within 4Å: Chain B: N.18, E.46, D.291 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.46, H2O.13, H2O.14, H2O.14, H2O.15 MG.12: 3 residues within 4Å: Chain C: N.18, E.46, D.291 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.46, H2O.26, H2O.26, H2O.26, H2O.27

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

CL.3: 3 residues within 4Å: Chain A: H.284, M.285, A.286 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: H.284, M.285, A.286 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain C: H.284, M.285, A.286 Ligand excluded by PLIP

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

SO4.4: 3 residues within 4Å: Chain A: S.50, K.51 Chain B: R.119 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.119, A:K.51, A:E.52 Water bridges: B:G.113, B:R.164, A:K.51, A:K.51 Salt bridges: A:K.51 SO4.9: 3 residues within 4Å: Chain B: S.50, K.51 Chain C: R.119 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.51, B:E.52, C:R.119 Water bridges: B:K.51, B:K.51, C:G.113, C:R.164 Salt bridges: B:K.51 SO4.14: 3 residues within 4Å: Chain A: R.119 Chain C: S.50, K.51 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:K.51, C:E.52, A:R.119 Water bridges: C:K.51, C:K.51, A:G.113, A:R.164 Salt bridges: C:K.51

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: Y.4, Q.6, F.8, H.100, Y.103, H.133, V.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.4, A:H.100 GOL.10: 7 residues within 4Å: Chain B: Y.4, Q.6, F.8, H.100, Y.103, H.133, V.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.4, B:Y.4, B:H.100 GOL.15: 7 residues within 4Å: Chain C: Y.4, Q.6, F.8, H.100, Y.103, H.133, V.305 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.4, C:Y.4, C:H.100

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

2014-04-16

Peptides

TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

TYPE II INOSITOL 1,4,5-TRISPHOSPHATE 5- PHOSPHATASE, ISOFORM 2

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