SMTL ID : 4g61.1

Crystal structure of IMPase/NADP phosphatase complexed with Mg2+ and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.94, D.97, D.215 Ligands: MG.2, PO4.3, GOL.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:D.97, A:D.215 MG.2: 7 residues within 4Å: Chain A: E.76, D.94, I.96, D.97 Ligands: MG.1, PO4.3, MG.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.76, A:D.94, A:I.96, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain A: K.42, L.48, E.76 Ligands: MG.2, PO4.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.76, H2O.1, H2O.1, H2O.1, H2O.1 MG.9: 6 residues within 4Å: Chain B: D.94, D.97, D.215 Ligands: PO4.8, MG.10, GOL.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.94, B:D.97, B:D.215 MG.10: 8 residues within 4Å: Chain B: E.76, D.94, I.96, D.97, T.99 Ligands: PO4.8, MG.9, MG.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.76, B:D.94, B:I.96, H2O.6, H2O.6 MG.11: 6 residues within 4Å: Chain B: K.42, D.47, L.48, E.76 Ligands: PO4.8, MG.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.76, H2O.6, H2O.6, H2O.6, H2O.6

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

PO4.3: 11 residues within 4Å: Chain A: E.76, D.94, I.96, D.97, G.98, T.99, D.215 Ligands: MG.1, MG.2, MG.4, GOL.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.98, A:T.99 Water bridges: A:D.47, A:D.53, A:T.99, A:T.99 PO4.8: 11 residues within 4Å: Chain B: E.76, D.94, I.96, D.97, G.98, T.99, D.215 Ligands: MG.9, MG.10, MG.11, GOL.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.98, B:T.99, B:T.99 Water bridges: B:I.96

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.97, G.98, G.189, A.190, C.191 Ligands: MG.1, PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.97, A:C.191, A:D.215 Water bridges: A:N.208 GOL.7: 4 residues within 4Å: Chain A: D.173, Q.176, D.177, N.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.173, A:D.177, A:D.177 GOL.12: 8 residues within 4Å: Chain B: D.97, G.98, G.189, A.190, C.191, D.215 Ligands: PO4.8, MG.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.97, B:D.97, B:G.98, B:C.191 Water bridges: B:N.166, B:N.166 GOL.15: 3 residues within 4Å: Chain B: D.173, Q.176, D.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.177

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

CL.6: 2 residues within 4Å: Chain A: L.193, R.197 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: L.193, R.197 Ligands: DTO.14 Ligand excluded by PLIP

1 x DTO: 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL(Non-covalent)

DTO.14: 10 residues within 4Å: Chain A: E.107, D.108, H.131, R.197 Chain B: E.107, D.108, H.131, V.188, R.197 Ligands: CL.13 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.131, A:R.197, B:H.131 Water bridges: A:K.133

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.16: 5 residues within 4Å: Chain B: F.68, P.69, E.70, H.71, H.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.70, B:E.70

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.17: 8 residues within 4Å: Chain A: M.150, E.151, K.200, G.201, Q.202 Chain B: K.104, Q.105, Q.106 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.151, B:K.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dutta, A. et al., Structural elucidation of the binding site and mode of inhibition of Li(+) and Mg(2+) in inositol monophosphatase. Febs J. (2014)

Release Date

2013-07-24

Peptides

Inositol monophosphatase family protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Inositol monophosphatase family protein

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