SMTL ID : 3itu.6 (5 other biounits)

hPDE2A catalytic domain complexed with IBMX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.86, H.122, D.123, D.234 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.234, H2O.1, H2O.1 ZN.4: 5 residues within 4Å: Chain B: H.86, H.122, D.123, D.234 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.86, B:H.122, B:D.123, B:D.234, H2O.18, H2O.18

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.123 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.123, H2O.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.5: 2 residues within 4Å: Chain B: D.123 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.123, H2O.18, H2O.18, H2O.18, H2O.18, H2O.18

2 x IBM: 3-ISOBUTYL-1-METHYLXANTHINE(Non-covalent)

IBM.3: 8 residues within 4Å: Chain A: Y.81, H.82, L.235, Q.238, I.252, Y.253, Q.285, F.288 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.81 Hydrogen bonds: A:Y.81, A:Q.285 Water bridges: A:Q.238 pi-Stacking: A:F.288, A:F.288 IBM.6: 9 residues within 4Å: Chain B: Y.81, H.82, L.196, L.235, Q.238, I.252, F.256, Q.285, F.288 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.81 Hydrogen bonds: B:Q.285 Water bridges: B:Q.238 pi-Stacking: B:F.288, B:F.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandit, J. et al., Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-10-27

Peptides

cGMP-dependent 3',5'-cyclic phosphodiesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

cGMP-dependent 3',5'-cyclic phosphodiesterase

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