SMTL ID : 4x0f.1

Crystal structure of crosslink stabilized long-form PDE4B in complex with (R)-(-)-rolipram

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.22 Å

Oligo State

homo-dimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.329, H.365, D.366, D.483 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.329, A:H.365, A:D.366, A:D.483 ZN.2: 2 residues within 4Å: Chain A: D.305, H.410 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.410 ZN.6: 4 residues within 4Å: Chain B: H.329, H.365, D.366, D.483 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.329, B:H.365, B:D.366, B:D.483

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

IOD.3: 1 residues within 4Å: Chain A: R.422 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain B: F.403, R.422 Ligand excluded by PLIP

2 x ROL: ROLIPRAM(Non-covalent)

ROL.4: 12 residues within 4Å: Chain A: Y.324, N.486, Y.494, W.497, T.498, I.501, F.505, S.533, Q.534, F.537 Chain B: Y.193, T.197 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.501, A:F.505, A:F.505, A:F.537, A:F.537 Hydrogen bonds: A:Q.534, B:Y.193 ROL.8: 15 residues within 4Å: Chain A: Y.193, T.197 Chain B: Y.324, M.438, N.486, Y.494, W.497, T.498, I.501, M.502, F.505, M.522, S.533, Q.534, F.537 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.505, B:F.505, B:F.537, B:F.537, B:F.537, A:Y.193 Hydrogen bonds: B:Q.534

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: H.365, D.366, E.395, H.398, T.436 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.366 MG.9: 3 residues within 4Å: Chain B: H.365, D.366, T.436 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.366

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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