1XM6: Catalytic Domain Of Human Phosphodiesterase 4B

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Mesopram. Determined by X-ray diffraction at 1.92 Å resolution. Released 14 Dec 2004.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,733
Mol. weight: 92.48 kDa
Ligands: ZN, MG, 5RM
Released: 14 Dec 2004

Explore 1XM6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1XM6 contains 51 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: 26 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	164-169	6
α-helix	170-172	3
α-helix	180-185	6
α-helix	191-202	12
α-helix	205-208	4
α-helix	213-225	13
α-helix	236-249	14
α-helix	253-255	3
α-helix	261-273	13
α-helix	283-288	6
α-helix	292-297	6
α-helix	302-315	14
α-helix	318-320	3
α-helix	328-343	16
α-helix	347-349	3
α-helix	350-362	13
β-strand	366	1	1
β-strand	372	1	1
α-helix	377-392	16
α-helix	395-397	3
α-helix	400-423	24
α-helix	426-429	4
α-helix	430-432	3
α-helix	439-446	8
α-helix	447-451	5
α-helix	452-461	10
α-helix	467-482	16
α-helix	500-511	12

Chain B: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	164-170	7
α-helix	180-186	7
α-helix	191-202	12
α-helix	205-208	4
α-helix	213-225	13
α-helix	236-249	14
α-helix	253-255	3
α-helix	261-273	13
α-helix	283-288	6
α-helix	292-297	6
α-helix	302-313	12
α-helix	318-320	3
α-helix	328-343	16
α-helix	347-349	3
α-helix	350-362	13
β-strand	366	1	2
β-strand	372	1	2
α-helix	377-392	16
α-helix	395-397	3
α-helix	400-423	24
α-helix	426-429	4
α-helix	430-432	3
α-helix	439-446	8
α-helix	447-451	5
α-helix	452-462	11
α-helix	467-482	16
α-helix	502-510	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A, B	protein	398	Homo sapiens	Q07343 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1XM6_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4B (chains A, B)
MGSSHHHHHHSSGLVPRGSHMSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNR
PLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLL
STPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAV
GFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSG
VLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISP
MCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSPSP
PLDEQNRDCQGLMEKFQFELTLDEEDSEGPEKEGEGHS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2
5RM	(5R)-5-(4-methoxy-3-propoxyphenyl)-5-methyl-1,3-oxazolidin-2-one	C14 H19 N O4	2

Primary citation

Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases. Card, G.L., England, B.P., Suzuki, Y. et al. Structure (2004) 12:2233-2247. DOI 10.1016/j.str.2004.10.004 · PubMed

Other PDB entries of the same protein (UniProt Q07343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KP6 1.5 Å, Crystal structure of human phosphodiesterase 4B (PDE4B) in complex with a…
2CHM 1.6 Å, Crystal structure of N2 substituted pyrazolo pyrimidinones - a flipped binding mode in…
5OHJ 1.6 Å, Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor.
3FRG 1.7 Å, Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with a Quinoline Inhibitor
6BOJ 1.7 Å, Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004
3D3P 1.75 Å, Crystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor
3GWT 1.75 Å, Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor
1F0J 1.77 Å, Catalytic domain of human phosphodiesterase 4B2B
5K6J 1.86 Å, Human Phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based inhibitor
8OEG 1.89 Å, PDE4B bound to MAPI compound 92a
4MYQ 1.9 Å, Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33
2QYL 1.95 Å, Crystal structure of PDE4B2B in complex with inhibitor NPV

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