3JWR: Chimeric PDE5/PDE6 catalytic domain

Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with 3-isobutyl-1-methylxanthine (IBMX) and PDE6 gamma-subunit inhibitory peptide 70-87. Determined by X-ray diffraction at 2.99 Å resolution. Released 13 Oct 2009.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,683
Mol. weight: 82.23 kDa
Ligands: IBM, MG, ZN
Released: 13 Oct 2009

Explore 3JWR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JWR contains 50 α-helices and 0 β-strands across 4 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, 0 β-strands

Element	Residues	Length
α-helix	538-543	6
α-helix	551-554	4
α-helix	568-581	14
α-helix	584-587	4
α-helix	592-604	13
α-helix	615-630	16
α-helix	635-637	3
α-helix	640-652	13
α-helix	662-667	6
α-helix	671-675	5
α-helix	680-693	14
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-795	24
α-helix	800-802	3
α-helix	803-805	3
α-helix	807-812	6
α-helix	813-820	8
α-helix	821-826	6
α-helix	827-835	9
α-helix	837-839	3
α-helix	840-857	18

Chain B: 24 helices, 0 β-strands

Element	Residues	Length
α-helix	533-543	11
α-helix	551-554	4
α-helix	568-581	14
α-helix	584-587	4
α-helix	592-604	13
α-helix	615-630	16
α-helix	635-637	3
α-helix	640-652	13
α-helix	662-667	6
α-helix	671-675	5
α-helix	680-693	14
α-helix	706-722	17
α-helix	725-740	16
α-helix	749-764	16
α-helix	766-769	4
α-helix	772-795	24
α-helix	800-802	3
α-helix	803-805	3
α-helix	807-812	6
α-helix	813-820	8
α-helix	821-826	6
α-helix	827-835	9
α-helix	837-839	3
α-helix	840-857	18

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	78-83	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic…	A, B	protein	330	Homo sapiens	O76074 (AlphaFold model), P51160 (AlphaFold model)
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma	C, D	protein	18	Homo sapiens	P18545 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3JWR_1 cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera (chains A, B)
GSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQM
KHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAA
LSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYK
TTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITK
PWPIQQRIAELVATEFWEQGDLERTVLQQQPIPMMDRNKRDELPKLQVGFIDFVCTQLYE
ALTHVSEDCFPLLDGCRKNRQKWQALAEQQ

Sequence of entity 2 (C, D), FASTA

>3JWR_2 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma (chains C, D)
WEAFNHLELHELAQYGII

Ligands and cofactors

ID	Name	Formula	Copies
IBM	3-isobutyl-1-methylxanthine	C10 H14 N4 O2	5
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit. Barren, B., Gakhar, L., Muradov, H. et al. EMBO J (2009) 28:3613-3622. DOI 10.1038/emboj.2009.284 · PubMed

Other PDB entries of the same protein (UniProt O76074 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TBF 1.3 Å, Catalytic Domain Of Human Phosphodiesterase 5A in Complex with Sildenafil
1XOZ 1.37 Å, Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Tadalafil
5JO3 1.49 Å, PDE5A for NaV1.7
2CHM 1.6 Å, Crystal structure of N2 substituted pyrazolo pyrimidinones - a flipped binding mode in…
1XP0 1.79 Å, Catalytic Domain Of Human Phosphodiesterase 5A In Complex With Vardenafil
3HC8 1.79 Å, Investigation of Aminopyridiopyrazinones as PDE5 Inhibitors: Evaluation of Modifications…
2H44 1.8 Å, Crystal structure of PDE5A1 in complex with icarisid II
3HDZ 1.8 Å, Identification, Synthesis, and SAR of Amino Substituted Pyrido[3,2b]pryaziones as Potent…
8W4S 1.85 Å, Crystal structure of PDE5A in complex with CVT-313
2H40 1.85 Å, Crystal structure of the catalytic domain of unliganded PDE5
3TGG 1.91 Å, A novel series of potent and selective PDE5 inhibitor2
6L6E 1.92 Å, Human PDE5 catalytic core in complex with avanafil

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