SMTL ID : 2yy2.1

Crystal structure of the human Phosphodiesterase 9A catalytic domain complexed with IBMX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.83, H.119, D.120, D.229 Ligands: MG.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.83, A:H.119, A:D.120, A:D.229 ZN.4: 6 residues within 4Å: Chain B: H.79, H.83, H.119, D.120, D.229 Ligands: MG.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.83, B:H.119, B:D.120, B:D.229

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.120, E.149, H.152, T.190 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.120 MG.5: 5 residues within 4Å: Chain B: D.120, E.149, H.152, T.190 Ligands: ZN.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.120

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

IBM.3: 7 residues within 4Å: Chain A: M.192, I.230, L.247, Y.251, A.279, Q.280, F.283 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.192, A:Y.251 Hydrogen bonds: A:Q.280 pi-Stacking: A:F.283, A:F.283 IBM.6: 8 residues within 4Å: Chain B: M.192, I.230, L.247, Y.251, F.268, A.279, Q.280, F.283 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.283 Hydrogen bonds: B:Y.251, B:Q.280 Water bridges: B:N.232 pi-Stacking: B:F.283, B:F.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Handa, N. et al., Crystal structure of the human Phosphodiesterase 9A catalytic domain. To be Published

Release Date

2007-10-30

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