3G4L	Hydrolase	date	Feb 03, 2009
title	Crystal Structure Of Human Phosphodiesterase 4d With Roflumi
authors	B.L.Staker
compound		source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d Chain: A, B, C, D Fragment: Residues 380-753 Synonym: Dpde3, Pde43 Ec: 3.1.4.17 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pde4d, Dpde3 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108 Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pbacgus
symmetry	Space Group: P 21 21 21	R_factor 0.214 R_Free 0.259
crystal cell	length a length b length c angle alpha angle beta angle gamma 99.665 111.952 161.701 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.50 Å
ligand	EDO, MG, ROF, SO4, ZN BindingDB	enzyme	Hydrolase E.C.3.1.4.17 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety., Burgin AB, Magnusson OT, Singh J, Witte P, Staker BL, Bjornsson JM, Thorsteinsdottir M, Hrafnsdottir S, Hagen T, Kiselyov AS, Stewart LJ, Gurney ME, Nat Biotechnol. 2009 Dec 27. PMID:20037581

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (222 Kb) [Save to disk] Biological Unit Coordinates (3g4l.pdb1.gz) 57 Kb Biological Unit Coordinates (3g4l.pdb2.gz) 56 Kb Biological Unit Coordinates (3g4l.pdb3.gz) 57 Kb Biological Unit Coordinates (3g4l.pdb4.gz) 58 Kb LPC: Ligand-Protein Contacts for 3G4L CSU: Contacts of Structural Units for 3G4L Structure Factors (968 Kb) Retrieve 3G4L in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3G4L from S2C, [Save to disk] Re-refined 3g4l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3G4L 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 3G4L

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 3G4L, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3g4l_B] [3g4l] [3g4l_D] [3g4l_C] [3g4l_A] SWISS-PROT database: [Q08499] Domain organization of [PDE4D_HUMAN] by SWISSPFAM Domain found in 3G4L: [HDc ] by SMART

Other resources with information on 3G4L

Community annotation for 3G4L at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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