SMTL ID : 3rl3.1

Rat metallophosphodiesterase MPPED2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: V.46, D.47, P.48, I.49, T.261, I.286, I.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.49 Water bridges: A:D.47, A:T.261

9 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: D.67, H.69, D.88, H.256 Ligands: MN.3, 5GP.12 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.67, A:H.69, A:D.88, A:H.256, H2O.5, 5GP.12 MN.3: 6 residues within 4Å: Chain A: D.67, D.88, N.119, H.215 Ligands: MN.2, 5GP.12 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.88, A:H.215, H2O.3, H2O.5, 5GP.12 MN.4: 3 residues within 4Å: Chain A: E.149, D.152, N.153 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.149, A:E.149, A:D.152, H2O.10 MN.5: 3 residues within 4Å: Chain A: E.207, G.208, V.245 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.207, A:V.245, H2O.2, H2O.9, H2O.9 MN.6: 3 residues within 4Å: Chain A: G.208, D.210 Ligands: MN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.208, A:D.210, H2O.12 MN.7: 2 residues within 4Å: Chain A: D.210 Ligands: MN.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.210 MN.8: 1 residues within 4Å: Chain A: D.47 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.47, H2O.10, H2O.10 MN.9: 1 residues within 4Å: Chain A: H.44 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.44, H2O.8, H2O.11 MN.10: 3 residues within 4Å: Chain A: N.186, W.188 Ligands: 5GP.12 No protein-ligand interaction detected (PLIP)

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

CL.11: 2 residues within 4Å: Chain A: R.222, R.231 Ligand excluded by PLIP

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.12: 18 residues within 4Å: Chain A: H.69, D.88, N.119, H.120, F.185, V.225, K.227, E.228, V.232, G.254, I.255, H.256, E.257, V.277, F.279 Ligands: MN.2, MN.3, MN.10 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.227, A:H.256, A:H.256, A:E.257 Water bridges: A:N.119, A:N.119, A:R.194, A:R.194 Salt bridges: A:H.69, A:H.120, A:H.256 pi-Stacking: A:F.185, A:F.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dermol, U. et al., Unique utilization of a phosphoprotein phosphatase fold by a mammalian phosphodiesterase associated with WAGR syndrome. J.Mol.Biol. (2011)

Release Date

2011-08-10

Peptides

Metallophosphoesterase MPPED2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallophosphoesterase MPPED2