SMTL ID : 3dyq.1 (1 other biounit)

human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cGMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 7 residues within 4Å: Chain A: H.75, H.79, H.115, D.116, D.225 Ligands: NA.2, PCG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.116 NA.2: 5 residues within 4Å: Chain A: H.115, D.116, D.225 Ligands: NA.1, PCG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.186, A:T.186 NA.4: 6 residues within 4Å: Chain B: H.75, H.79, H.115, D.116, D.225 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.116 NA.5: 3 residues within 4Å: Chain B: D.116, E.145 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.116

1 x PCG: CYCLIC GUANOSINE MONOPHOSPHATE(Non-covalent)

PCG.3: 13 residues within 4Å: Chain A: H.75, D.116, T.186, M.188, D.225, I.226, L.243, Y.247, A.275, Q.276, F.279 Ligands: NA.1, NA.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.116, A:Y.247, A:Q.276, A:Q.276, A:Q.276 Water bridges: A:E.145 Salt bridges: A:H.75 pi-Stacking: A:F.279 pi-Cation interactions: A:F.279

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

IBM.6: 8 residues within 4Å: Chain B: M.188, I.226, L.243, Y.247, F.264, A.275, Q.276, F.279 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.247 Water bridges: B:Q.276 pi-Stacking: B:F.279, B:F.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Structural basis for the catalytic mechanism of human phosphodiesterase 9. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-09-16

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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