1F0J | pdb_00001f0j

CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B2B

PDB DOI: https://doi.org/10.2210/pdb1F0J/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): Yes

Deposited: 2000-05-16 Released: 2000-07-26
Deposition Author(s): Xu, R.X., Hassell, A.M., Vanderwall, D., Lambert, M.H., Holmes, W.D., Luther, M.A., Rocque, W.J., Milburn, M.V., Zhao, Y., Ke, H., Nolte, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.223 (Depositor)
R-Value Work:
0.204 (Depositor)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Atomic structure of PDE4: insights into phosphodiesterase mechanism and specificity.

Xu, R.X., Hassell, A.M., Vanderwall, D., Lambert, M.H., Holmes, W.D., Luther, M.A., Rocque, W.J., Milburn, M.V., Zhao, Y., Ke, H., Nolte, R.T.

(2000) Science 288: 1822-1825

PubMed: 10846163 Search on PubMed
DOI: https://doi.org/10.1126/science.288.5472.1822
Primary Citation Related Structures:
1F0J

PubMed Abstract:
Cyclic nucleotides are second messengers that are essential in vision, muscle contraction, neurotransmission, exocytosis, cell growth, and differentiation. These molecules are degraded by a family of enzymes known as phosphodiesterases, which serve a critical function by regulating the intracellular concentration of cyclic nucleotides. We have determined the three-dimensional structure of the catalytic domain of phosphodiesterase 4B2B to 1.77 angstrom resolution. The active site has been identified and contains a cluster of two metal atoms. The structure suggests the mechanism of action and basis for specificity and will provide a framework for structure-assisted drug design for members of the phosphodiesterase family.

Organizational Affiliation

Department of Structural Chemistry, Department of Molecular Sciences, Glaxo Wellcome Research and Development, Research Triangle Park, NC 27709, USA.

Macromolecule Content

Total Structure Weight: 87.2 kDa
Atom Count: 6,318
Modeled Residue Count: 688
Deposited Residue Count: 754
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHODIESTERASE 4B	A, B	377	Homo sapiens	Mutation(s): 2 EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens) Explore Q07343 Go to UniProtKB: Q07343
PHAROS: Q07343 GTEx: ENSG00000184588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q07343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARS Query on ARS Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B]