5K1I	Hydrolase	date	May 18, 2016
title	Pde4 Crystal Structure In Complex With Small Molecule Inhibi
authors	V.Segarra, B.Hernandez, N.Ferrer-Miralles, I.Korndoerfer, J.Ayma
compound		source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d Chain: A, B, C, D, E, F, G, H Synonym: Dpde3,Pde43 Ec: 3.1.4.53 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pde4d, Dpde3 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008
symmetry	Space Group: P 1	R_factor 0.191 R_Free 0.258
crystal cell	length a length b length c angle alpha angle beta angle gamma 61.444 78.347 161.756 91.01 92.79 90.08
method	X-Ray Diffraction	resolution	2.61 Å
ligand	6PT, MG, ZN	enzyme	Hydrolase E.C.3.1.4.53 BRENDA
Gene Ontology	Chain Function Process Component F, A, E, B, H, C, D, G
Primary reference	Biphenyl Pyridazinone Derivatives as Inhaled PDE4 Inhibitors: Structural Biology and Structure-Activity Relationships., Gracia J, Buil MA, Castro J, Eichhorn P, Ferrer M, Gavalda A, Hernandez B, Segarra V, Lehner MD, Moreno I, Pages L, Roberts RS, Serrat J, Sevilla S, Taltavull J, Andres M, Cabedo J, Vilella D, Calama E, Carcasona C, Miralpeix M, J Med Chem. 2016 Dec 8;59(23):10479-10497. Epub 2016 Nov 17. PMID:27933955

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (863 Kb) [Save to disk] Biological Unit Coordinates (5k1i.pdb1.gz) 112 Kb Biological Unit Coordinates (5k1i.pdb2.gz) 112 Kb Biological Unit Coordinates (5k1i.pdb3.gz) 111 Kb Biological Unit Coordinates (5k1i.pdb4.gz) 112 Kb Biological Unit Coordinates (5k1i.pdb5.gz) 111 Kb Biological Unit Coordinates (5k1i.pdb6.gz) 114 Kb Biological Unit Coordinates (5k1i.pdb7.gz) 111 Kb Biological Unit Coordinates (5k1i.pdb8.gz) 112 Kb LPC: Ligand-Protein Contacts for 5K1I CSU: Contacts of Structural Units for 5K1I Structure Factors (1190 Kb) Retrieve 5K1I in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5K1I from S2C, [Save to disk] Re-refined 5k1i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5K1I 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 5K1I

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5k1i_H] [5k1i_B] [5k1i_E] [5k1i_F] [5k1i_G] [5k1i_C] [5k1i_D] [5k1i] [5k1i_A] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5K1I

Community annotation for 5K1I at PDBWiki (http://pdbwiki.org)

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