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1mkd

crystal structure of PDE4D catalytic domain and zardaverine complex

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

Phosphodiesterase 4D

Homo sapiens

UniProt Q08499

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 6 ZINC ION × 6 MAGNESIUM ION × 6 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHENYL)-2H-PYRIDAZIN-3-ONE × 6 water × 6 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 6 ZINC ION × 6 MAGNESIUM ION × 6 6-(4-DIFLUOROMETHOXY-3-METHOXY-PHENYL)-2H-PYRIDAZIN-3-ONE × 6 water × 6 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 —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–328； UniProt 388–715 Author chain B； PDBConstruct 1–328； UniProt 388–715 Author chain C； PDBConstruct 1–328； UniProt 388–715 Author chain D； PDBConstruct 1–328； UniProt 388–715 Author chain E； PDBConstruct 1–328； UniProt 388–715 Author chain F； PDBConstruct 1–328； UniProt 388–715 Author chain G； PDBConstruct 1–328； UniProt 388–715 Author chain H； PDBConstruct 1–328； UniProt 388–715 Author chain I； PDBConstruct 1–328； UniProt 388–715 Author chain J； PDBConstruct 1–328； UniProt 388–715 Author chain K； PDBConstruct 1–328； UniProt 388–715 Author chain L； PDBConstruct 1–328； UniProt 388–715

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_id1mkd
Deposition date deposition_date2002-08-29
Structure title titlecrystal structure of PDE4D catalytic domain and zardaverine complex
Keywords keywordsPDE, Zardaverine, Hydrolase; 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.

1mkd__assembly_1__model_1

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

Download this curve (.dat)

1mkd__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1mkd__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）39.95 Å
Rg (electron density)38.97 Å
Total Rg39.38 Å
Atom count16026
Residues1968
Excluded volume284450 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1mkd__assembly_1__model_1 hexameric （6） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1mkd__assembly_2__model_1 hexameric （6） 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) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1mkda_
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_idd1mkdb_
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_idd1mkdc_
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_idd1mkdd_
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_idd1mkde_
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_idd1mkdf_
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_idd1mkdg_
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_idd1mkdh_
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_idd1mkdi_
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_idd1mkdj_
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_idd1mkdk_
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_idd1mkdl_
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 (12 domains)

Domain ID domain_id1mkdA00
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_id1mkdB00
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_id1mkdC00
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_id1mkdD00
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_id1mkdE00
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_id1mkdF00
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_id1mkdG00
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_id1mkdH00
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_id1mkdI00
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_id1mkdJ00
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_id1mkdK00
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_id1mkdL00
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)