2PW3: PDE4D-cAMP complex

Structure of the PDE4D-cAMP complex. Determined by X-ray diffraction at 1.56 Å resolution. Released 23 Oct 2007.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,854
Mol. weight: 76.2 kDa
Ligands: CMP, ZN
Released: 23 Oct 2007

Explore 2PW3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PW3 contains 48 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	88-95	8
α-helix	96-98	3
α-helix	106-112	7
α-helix	117-128	12
α-helix	131-134	4
α-helix	139-151	13
α-helix	162-176	15
α-helix	179-181	3
α-helix	187-199	13
α-helix	209-214	6
α-helix	218-222	5
α-helix	228-239	12
α-helix	240-242	3
α-helix	254-269	16
α-helix	273-275	3
α-helix	276-288	13
β-strand	292	1	1
β-strand	298	1	1
α-helix	303-318	16
α-helix	321-323	3
α-helix	326-349	24
α-helix	352-355	4
α-helix	365-372	8
α-helix	373-377	5
α-helix	378-387	10
α-helix	393-408	16

Chain B: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	89-95	7
α-helix	96-98	3
α-helix	106-112	7
α-helix	117-128	12
α-helix	131-134	4
α-helix	139-151	13
α-helix	162-175	14
α-helix	179-181	3
α-helix	187-199	13
α-helix	209-214	6
α-helix	218-223	6
α-helix	228-239	12
α-helix	240-242	3
α-helix	254-269	16
α-helix	273-275	3
α-helix	276-288	13
β-strand	292	1	2
β-strand	298	1	2
α-helix	303-318	16
α-helix	321-323	3
α-helix	326-350	25
α-helix	352-355	4
α-helix	365-372	8
α-helix	373-377	5
α-helix	378-387	10
α-helix	393-408	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B	protein	327	Homo sapiens	Q08499 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2PW3_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D (chains A, B)
TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITY
LMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHNVDHP
GVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVI
DIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKP
LQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWA
DLVHPDAQDILDTLEDNREWYQSTIPQ

Ligands and cofactors

ID	Name	Formula	Copies
CMP	Adenosine-3',5'-cyclic-monophosphate	C10 H12 N5 O6 P	2
ZN	Zinc ion	Zn	2

Primary citation

The molecular basis for different recognition of substrates by phosphodiesterase families 4 and 10. Wang, H., Robinson, H., Ke, H. J Mol Biol (2007) 371:302-307. DOI 10.1016/j.jmb.2007.05.060 · PubMed

Other PDB entries of the same protein (UniProt Q08499 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Y2K 1.36 Å, Catalytic Domain Of Human Phosphodiesterase 4D In Complex With…
8W4R 1.37 Å, Crystal structure of PDE4D complexed with CVT-313
1Y2B 1.4 Å, Catalytic Domain Of Human Phosphodiesterase 4D In Complex With…
6FDC 1.45 Å, Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a
6LRM 1.45 Å, Crystal structure of PDE4D catalytic domain in complex with arctigenin
6IMI 1.46 Å, Crystal structure of PDE4D complexed with a novel inhibitor
6IMT 1.48 Å, Crystal structure of PDE4D complexed with a novel inhibitor
6IMD 1.5 Å, Crystal structure of PDE4D complexed with a novel inhibitor
7B9H 1.5 Å, Crystal structure of the PDE4D catalytic domain in complex with GEBR-42a
7CBJ 1.5 Å, Crystal structure of PDE4D catalytic domain in complex with compound 36
6IMR 1.5 Å, Crystal structure of PDE4D complexed with a novel inhibitor
1XOR 1.54 Å, Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Zardaverine

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