1PTW	Hydrolase	date	Jun 23, 2003
title	The Crystal Structure Of Amp-Bound Pde4 Suggests A Mechanism Phosphodiesterase Catalysis
authors	Q.Huai, J.Colicelli, H.Ke
compound		source
Molecule: Camp-Specific Phosphodiesterase Pde4d2 Chain: A, B, C, D Fragment: Catalytic Domain Synonym: Dpde3, Pde43, Pde4d2 Ec: 3.1.4.17 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pde4d2 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-15b
symmetry	Space Group: P 21 21 21	R_factor 0.229 R_Free 0.274
crystal cell	length a length b length c angle alpha angle beta angle gamma 99.207 111.229 159.650 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	AMP, ZN	enzyme	Hydrolase E.C.3.1.4.17 BRENDA
related structures	by homologous chain: 1Q9M, 1XN0
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis., Huai Q, Colicelli J, Ke H, Biochemistry 2003 Nov 18;42(45):13220-6. PMID:14609333

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (220 Kb) [Save to disk] Biological Unit Coordinates (1ptw.pdb1.gz) 213 Kb LPC: Ligand-Protein Contacts for 1PTW CSU: Contacts of Structural Units for 1PTW Likely Quarternary Molecular Structure file(s) for 1PTW Structure Factors (1005 Kb) Retrieve 1PTW in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1PTW from S2C, [Save to disk] Re-refined 1ptw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1PTW in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1PTW

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1PTW, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1ptwa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1ptwb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1ptwc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1ptwd_, region D [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ptw] [1ptw_A] [1ptw_D] [1ptw_B] [1ptw_C] SWISS-PROT database: [Q08499] Domain organization of [PDE4D_HUMAN] by SWISSPFAM Domain found in 1PTW: [HDc ] by SMART

Other resources with information on 1PTW

Community annotation for 1PTW at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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