SMTL ID : 3n3z.1

Crystal structure of PDE9A (E406A) mutant in complex with IBMX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

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

IBM.1: 8 residues within 4Å: Chain A: F.71, I.223, N.225, L.240, Y.244, A.272, Q.273, F.276 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.240, A:Y.244, A:A.272 Hydrogen bonds: A:N.225, A:Q.273 pi-Stacking: A:F.276 IBM.6: 8 residues within 4Å: Chain B: M.185, I.223, L.240, Y.244, F.261, A.272, Q.273, F.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.244 pi-Stacking: B:F.276, B:F.276

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.76, H.112, D.113, D.222 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.76, A:H.112, A:D.113, A:D.222 ZN.4: 6 residues within 4Å: Chain B: H.72, H.76, H.112, D.113, D.222 Ligands: MG.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.76, B:H.112, B:D.113, B:D.222, H2O.4

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.113, H.145 Ligands: ZN.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.113, H2O.2, H2O.2, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain B: D.113 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.113, H2O.4, H2O.4, H2O.4, H2O.4

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

CL.7: 1 residues within 4Å: Chain B: R.307 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, J. et al., Crystal structure of PDE9A (E406A) mutation in complex with IBMX. To be Published

Release Date

2011-04-13

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