1XLZ: Catalytic Domain Of Human Phosphodiesterase 4B

Catalytic Domain Of Human Phosphodiesterase 4B In Complex With Filaminast. Determined by X-ray diffraction at 2.06 Å resolution. Released 14 Dec 2004.

Method: X-ray diffraction
Resolution: 2.06 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,424
Mol. weight: 92.38 kDa
Ligands: FIL, MG, ZN
Released: 14 Dec 2004

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

Secondary structure: helices and β-sheets

1XLZ 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	164-170	7
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	292-296	5
α-helix	302-314	13
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

Chain B: 24 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

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

>1XLZ_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
FIL	(1E)-1-[3-(cyclopentyloxy)-4-methoxyphenyl]ethanone O-(aminocarbonyl)oxime	C15 H20 N2 O4	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	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
1XM6 1.92 Å, Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Mesopram

Browse structure collections

About this viewer

MolViewer shows 1XLZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.