5K6J: Human Phospodiesterase 4B

Human Phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based inhibitor. Determined by X-ray diffraction at 1.86 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,898
Mol. weight: 38.86 kDa
Ligands: 6QQ, MG, ZN
Released: 31 May 2017

Explore 5K6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5K6J contains 24 α-helices and 2 β-strands across 1 chain. 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	163-169	7
α-helix	170-172	3
α-helix	180-186	7
α-helix	191-202	12
α-helix	205-208	4
α-helix	213-225	13
α-helix	236-250	15
α-helix	253-255	3
α-helix	261-273	13
α-helix	283-288	6
α-helix	292-296	5
α-helix	302-313	12
α-helix	314-316	3
α-helix	328-343	16
α-helix	347-349	3
α-helix	350-362	13
β-strand	365-366	2	1
β-strand	372-373	2	1
α-helix	377-392	16
α-helix	395-397	3
α-helix	400-423	24
α-helix	426-429	4
α-helix	439-446	8
α-helix	447-451	5
α-helix	452-461	10
α-helix	467-482	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	protein	323	Homo sapiens	Q07343 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5K6J_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4B (chains A)
NEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMM
TLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGV
SNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDM
VLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLE
LYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADL
VQPDAQDILDTLEDNRNWYQSMI

Ligands and cofactors

ID	Name	Formula	Copies
6QQ	6-[[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl]o…	C18 H17 B Cl N2 O6	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

To be published. Dong, C., Jarnagin, K. To be published.

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
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
2QYL 1.95 Å, Crystal structure of PDE4B2B in complex with inhibitor NPV

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