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6boj

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004

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

;cAMP-specific 3',5'-cyclic phosphodiesterase 4D ;

Homo sapiens

UniProt Q07343

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 × 2 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 water × 1 Consistent with protein count
2 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1 Consistent with protein count
3 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1 Consistent with protein count
4 Insufficient information Monomer Protein 1 ZINC ION × 2 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 water × 1 Consistent with protein count
5 Insufficient information Homooligomer Protein 4 ZINC ION × 6 MAGNESIUM ION × 4 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 4 CHLORIDE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1f0j 1f0j 1ro6 1ro6 1ro9 1ro9 1ror 1ror 1tb5 1tb5 1xlx 1xlx

65 assemblies; showing the first 12

Homodimer
3frg 3g45 3gwt 3kkt 4wzi 4x0f

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2chm 6boj 6boj 6boj 6boj 6boj

6 assemblies

View Construct and Data Evidence
UniProt name PDE4B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 337–350； UniProt 659–672 Author chain B； PDBConstruct 337–350； UniProt 659–672 Author chain C； PDBConstruct 337–350； UniProt 659–672 Author chain D； PDBConstruct 337–350； UniProt 659–672

;cAMP-specific 3',5'-cyclic phosphodiesterase 4D ;

Homo sapiens

UniProt Q08499

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 × 2 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 water × 1 Consistent with protein count
2 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1 Consistent with protein count
3 Insufficient information Monomer Protein 1 ZINC ION × 1 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1 Consistent with protein count
4 Insufficient information Monomer Protein 1 ZINC ION × 2 MAGNESIUM ION × 1 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 1 CHLORIDE ION × 1 water × 1 Consistent with protein count
5 Insufficient information Homooligomer Protein 4 ZINC ION × 6 MAGNESIUM ION × 4 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide × 4 CHLORIDE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1e9k 1tb7 1tb7 1tbb 1tbb 1xom 1xom 1xon 1xon 1xoq 1xoq 1xor

203 assemblies; showing the first 12

Homodimer
2pw3 2qyn 3iak 3k4s 4w1o 4w1o 5k32 6f6u 6f8r 6f8t 6f8u 6f8v

50 assemblies; showing the first 12

Homotetramer
1oyn 1ptw 1q9m 1zkn 2fm0 2fm5 4wcu 6zba

8 assemblies

Other homooligomers
1mkd 1mkd

2 assemblies

Heteromeric or nucleic-acid complex
6boj 6boj 6boj 6boj 6boj

5 assemblies

View Construct and Data Evidence
UniProt name PDE4D_HUMAN
Isoform Q08499-8
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–336； UniProt 89–423 Author chain A； PDBConstruct 351–364； UniProt 326–339 Author chain B； PDBConstruct 2–336； UniProt 89–423 Author chain B； PDBConstruct 351–364； UniProt 326–339 Author chain C； PDBConstruct 2–336； UniProt 89–423 Author chain C； PDBConstruct 351–364； UniProt 326–339 Author chain D； PDBConstruct 2–336； UniProt 89–423 Author chain D； PDBConstruct 351–364； UniProt 326–339

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_id6boj
Deposition date deposition_date2017-11-20
Structure title titleCrystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004
Keywords keywords;PDE4D, CAMP-SPECIFIC 3'5'-CYCLIC PHOSPHODIESTERASE 4D, UCR2, CAMP, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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.

6boj__assembly_1__model_1

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

Download this curve (.dat)

6boj__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.

6boj__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）20.47 Å
Rg (electron density)19.25 Å
Total Rg20.19 Å
Atom count2675
Residues335
Excluded volume47548 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6boj__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6boj__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6boj__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6boj__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 6boj__assembly_5__model_1 tetrameric （4） 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 (7)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6boja_
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_idd6bojb_
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_idd6bojc_
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_idd6bojd_
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_id6bojA00
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_id6bojB00
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_id6bojC00
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_id6bojD00
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)