SMTL ID : 3mmj.1

Structure of the PTP-like phytase from Selenomonas ruminantium in complex with myo-inositol hexakisphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 19 residues within 4Å: Chain A: R.25, D.121, K.157, D.191, H.192, S.220, E.221, A.222, G.223, V.224, G.225, R.226, F.257, K.273, Y.277, K.280 Ligands: PO4.2, ACT.3, GOL.6 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:D.191, A:S.220, A:E.221, A:A.222, A:G.223, A:V.224, A:G.225, A:R.226, A:Y.277, A:Y.277 Water bridges: A:R.25, A:K.51, A:K.51, A:K.51, A:K.157, A:K.157, A:K.157, A:H.192, A:Y.259, A:K.273, A:K.273, A:K.273, A:K.280 Salt bridges: A:R.25, A:R.25, A:K.51, A:K.157, A:K.157, A:K.157, A:H.192, A:H.192, A:R.226, A:K.273, A:K.280 IHP.7: 19 residues within 4Å: Chain B: R.25, D.121, K.157, D.191, H.192, S.220, E.221, A.222, G.223, V.224, G.225, R.226, F.257, K.273, Y.277, K.280 Ligands: PO4.8, ACT.9, GOL.12 32 PLIP interactions: 32 interactions with chain B Hydrogen bonds: B:D.191, B:S.220, B:E.221, B:A.222, B:G.223, B:V.224, B:G.225, B:R.226, B:Y.277, B:Y.277 Water bridges: B:R.25, B:K.51, B:K.51, B:K.157, B:K.157, B:H.192, B:K.273, B:K.273, B:K.273, B:K.273, B:K.280 Salt bridges: B:R.25, B:R.25, B:K.51, B:K.157, B:K.157, B:K.157, B:H.192, B:H.192, B:R.226, B:K.273, B:K.280

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

PO4.2: 9 residues within 4Å: Chain A: D.191, S.220, E.221, A.222, G.223, V.224, G.225, R.226 Ligands: IHP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.220, A:E.221, A:A.222, A:G.223, A:V.224, A:G.225, A:R.226 Salt bridges: A:R.226 PO4.8: 9 residues within 4Å: Chain B: D.191, S.220, E.221, A.222, G.223, V.224, G.225, R.226 Ligands: IHP.7 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.220, B:E.221, B:A.222, B:G.223, B:V.224, B:G.225, B:R.226 Water bridges: B:D.191, B:R.226 Salt bridges: B:R.226

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 6 residues within 4Å: Chain A: H.192, K.273, Y.276, Y.277, K.280 Ligands: IHP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.273, A:Y.276, A:Y.277 Water bridges: A:Y.277 Salt bridges: A:H.192, A:K.273, A:K.280 ACT.4: 4 residues within 4Å: Chain A: Y.10, R.278, E.279, A.314 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.10 Hydrogen bonds: A:Y.10 ACT.9: 6 residues within 4Å: Chain B: H.192, K.273, Y.276, Y.277, K.280 Ligands: IHP.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:K.273, B:Y.276, B:Y.277 Water bridges: B:Y.277 Salt bridges: B:H.192, B:K.273, B:K.280 ACT.10: 4 residues within 4Å: Chain B: Y.10, R.278, E.279, A.314 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.10, B:A.314 Hydrogen bonds: B:Y.10, B:Y.10 Salt bridges: B:R.278

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: Y.207, P.211, Q.212, A.214, K.238 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.207, A:Q.212, A:A.214 Water bridges: A:H.69, A:K.238, A:K.238 GOL.6: 7 residues within 4Å: Chain A: K.51, F.257, F.262, I.264, K.265, Y.277 Ligands: IHP.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.51, A:K.265, A:K.265 Water bridges: A:K.51, A:Y.277 GOL.11: 7 residues within 4Å: Chain B: L.68, Y.207, P.211, Q.212, A.214, K.238 Ligands: GOL.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.68, B:Y.207, B:Q.212 Water bridges: B:H.69, B:K.238, B:K.238 GOL.12: 7 residues within 4Å: Chain B: K.51, F.257, F.262, I.264, K.265, Y.277 Ligands: IHP.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.51, B:K.265, B:K.265 Water bridges: B:P.263, B:Y.277 GOL.13: 4 residues within 4Å: Chain B: L.210, P.211, Q.212 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.212, B:Q.212 Water bridges: B:L.210

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

CL.14: 1 residues within 4Å: Chain B: T.301 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gruninger, R.J. et al., Substrate binding in protein-tyrosine phosphatase-like inositol polyphosphatases. J.Biol.Chem. (2012)

Release Date

2011-06-15

Peptides

Myo-inositol hexaphosphate phosphohydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Myo-inositol hexaphosphate phosphohydrolase