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3jwq

Crystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

Homo sapiens

UniProt O76074

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count
2 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count
3 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count
4 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1rkp 1t9r 1t9s 1t9s 1tbf 1udt 1uho 1xoz 1xp0 2h40 2h42 2h42

47 assemblies; showing the first 12

Homodimer
1udu 2h40 2h42 3lfv 3mf0

5 assemblies

Homotetramer
2xss

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2chm 3hc8 3hdz 3jwq 3jwq 3jwq 3jwq 3jwr 3jwr

9 assemblies

View Construct and Data Evidence
UniProt name PDE5A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–256； UniProt 535–786 Author chain A； PDBConstruct 297–330； UniProt 827–860 Author chain B； PDBConstruct 5–256； UniProt 535–786 Author chain B； PDBConstruct 297–330； UniProt 827–860 Author chain C； PDBConstruct 5–256； UniProt 535–786 Author chain C； PDBConstruct 297–330； UniProt 827–860 Author chain D； PDBConstruct 5–256； UniProt 535–786 Author chain D； PDBConstruct 297–330； UniProt 827–860

;cGMP-specific 3',5'-cyclic phosphodiesterase catalytic domain, Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha chimera ;

Homo sapiens

UniProt P51160

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count
2 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count
3 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count
4 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3jwq 3jwq 3jwq 3jwq 3jwr 3jwr 5e8f 5e8f 9cxg 9cxh 9cxi 9cxj

12 assemblies

View Construct and Data Evidence
UniProt name PDE6C_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 257–296； UniProt 746–785 Author chain B； PDBConstruct 257–296； UniProt 746–785 Author chain C； PDBConstruct 257–296； UniProt 746–785 Author chain D； PDBConstruct 257–296； UniProt 746–785

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3jwq
Deposition date deposition_date2009-09-18
Structure title titleCrystal structure of chimeric PDE5/PDE6 catalytic domain complexed with sildenafil
Keywords keywords;mostly alpha, Allosteric enzyme, cGMP, cGMP-binding, Hydrolase, Magnesium, Metal-binding, Nucleotide-binding, Phosphoprotein, Cell membrane, Lipoprotein, Membrane, Methylation, Prenylation, Sensory transduction, Vision ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3jwq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3jwq__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3jwq__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.86 Å
Rg (electron density)19.66 Å
Total Rg20.57 Å
Atom count2673
Residues324
Excluded volume47826 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3jwq__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3jwq__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3jwq__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3jwq__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3jwqa_
Class classa — All alpha proteins
Fold Fold folda.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamilya.211.1 — HD-domain/PDEase-like
Family Family familya.211.1.2 — PDEase
Domain ID domain_idd3jwqb_
Class classa — All alpha proteins
Fold Fold folda.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamilya.211.1 — HD-domain/PDEase-like
Family Family familya.211.1.2 — PDEase
Domain ID domain_idd3jwqc1
Class classa — All alpha proteins
Fold Fold folda.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamilya.211.1 — HD-domain/PDEase-like
Family Family familya.211.1.2 — PDEase
Domain ID domain_idd3jwqc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3jwqd_
Class classa — All alpha proteins
Fold Fold folda.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamilya.211.1 — HD-domain/PDEase-like
Family Family familya.211.1.2 — PDEase

CATH v4.4 (4 domains)

Domain ID domain_id3jwqA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain
Domain ID domain_id3jwqB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain
Domain ID domain_id3jwqC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain
Domain ID domain_id3jwqD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1300 — Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
Homologous superfamily homologous superfamily10 — 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain
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7. Citations (1)