SMTL ID : 3qi4.1

Crystal structure of PDE9A(Q453E) in complex with IBMX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

IBM.1: 7 residues within 4Å: Chain A: M.365, I.403, L.420, Y.424, F.441, E.453, F.456 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.441, A:F.456 pi-Stacking: A:F.456, A:F.456 IBM.4: 8 residues within 4Å: Chain B: M.365, I.403, L.420, Y.424, F.441, A.452, E.453, F.456 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.456 Hydrogen bonds: B:Y.424 Water bridges: B:A.452 pi-Stacking: B:F.456, B:F.456

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.256, H.292, D.293, D.402 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.256, A:H.292, A:D.293, A:D.402, H2O.1 ZN.5: 5 residues within 4Å: Chain B: H.256, H.292, D.293, D.402 Ligands: MG.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.256, B:H.292, B:D.293, B:D.402, H2O.1

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: H.252, D.293 Ligands: ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.293, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: H.292, D.293 Ligands: ZN.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.293, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, J. et al., Structural asymmetry of phosphodiesterase-9, potential protonation of a glutamic Acid, and role of the invariant glutamine. Plos One (2011)

Release Date

2011-04-27

Peptides

High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A

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