SMTL ID : 4wzi.1

Crystal structure of crosslink stabilized long-form PDE4B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

homo-dimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.329, H.365, D.366, D.483 Ligands: MG.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.329, A:H.365, A:D.366, A:D.483, H2O.8 ZN.2: 1 residues within 4Å: Chain A: H.410 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.410, H2O.1 ZN.6: 5 residues within 4Å: Chain B: H.329, H.365, D.366, D.483 Ligands: MG.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.329, B:H.365, B:D.366, B:D.483, H2O.13

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

NA.3: 4 residues within 4Å: Chain A: E.315, D.316, Y.318, S.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.320, A:S.320 Water bridges: A:D.316, A:D.316 NA.7: 3 residues within 4Å: Chain B: D.316, Y.318, S.320 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.316, B:S.320

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain A: D.366 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.366, H2O.2, H2O.3, H2O.8, H2O.8 MG.8: 2 residues within 4Å: Chain B: D.366 Ligands: ZN.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.366, H2O.9, H2O.9, H2O.13, H2O.13

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 2 residues within 4Å: Chain A: F.403, R.422 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain B: F.403, R.422 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cedervall, P. et al., Engineered stabilization and structural analysis of the autoinhibited conformation of PDE4. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-03-11

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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