SMTL ID : 1zkn.1

Structure of PDE4D2-IBMX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.86, H.122, D.123, D.240 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.86, A:H.122, A:D.123, A:D.240, H2O.1 ZN.4: 5 residues within 4Å: Chain B: H.86, H.122, D.123, D.240 Ligands: MG.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.86, B:H.122, B:D.123, B:D.240, H2O.3 ZN.7: 5 residues within 4Å: Chain C: H.86, H.122, D.123, D.240 Ligands: MG.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.86, C:H.122, C:D.123, C:D.240 ZN.10: 5 residues within 4Å: Chain D: H.86, H.122, D.123, D.240 Ligands: MG.11 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.86, D:H.122, D:D.123, D:D.240, H2O.7

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.123 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.123, H2O.2, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain B: D.123 Ligands: ZN.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.123, H2O.3, H2O.3, H2O.3 MG.8: 2 residues within 4Å: Chain C: D.123 Ligands: ZN.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.123, H2O.4, H2O.5, H2O.5 MG.11: 2 residues within 4Å: Chain D: D.123 Ligands: ZN.10 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.123, H2O.6, H2O.7, H2O.7, H2O.7

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

IBM.3: 5 residues within 4Å: Chain A: I.258, F.262, M.279, Q.291, F.294 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.262 Hydrogen bonds: A:Q.291 Water bridges: A:N.243 pi-Stacking: A:F.262, A:F.294 IBM.6: 5 residues within 4Å: Chain B: M.195, F.262, M.279, Q.291, F.294 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:M.195 Hydrogen bonds: B:Q.291 Water bridges: B:N.243 pi-Stacking: B:F.262, B:F.294 IBM.9: 6 residues within 4Å: Chain C: M.195, L.241, I.258, M.279, Q.291, F.294 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:M.195 Hydrogen bonds: C:Q.291 pi-Stacking: C:F.294 IBM.12: 7 residues within 4Å: Chain D: Y.81, M.195, I.258, F.262, M.279, Q.291, F.294 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.294 Hydrogen bonds: D:Q.291 pi-Stacking: D:F.262, D:F.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huai, Q. et al., Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor 3-Isobutyl-1-Methylxanthine Suggest a Conformation Determinant of Inhibitor Selectivity. J.Biol.Chem. (2004)

Release Date

2005-05-17

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

cAMP-specific 3',5'-cyclic phosphodiesterase 4D

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