1Y2D Hydrolase date Nov 22, 2004
title Catalytic Domain Of Human Phosphodiesterase 4d In Complex Wi Methoxy-Phenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ester
authors G.L.Card, L.Blasdel, B.P.England, C.Zhang, Y.Suzuki, S.Gillette, D P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.H.Kim, J.Schle K.Y.J.Zhang
compound source
Molecule: Camp-Specific 3',5'-Cyclic Phosphodiesterase 4d
Chain: A, B
Fragment: Catalytic Domain Of Human Phosphodiesterase 4d
Synonym: Dpde3, Pde43
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde4d
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codon Plus(Ril)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.165 R_Free 0.189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.804 79.146 164.617 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand 4DE, B3P, EDO, MG, ZN BindingDB enzyme Hydrolase E.C.3.1.4.17 BRENDA
related structures by homologous chain: 1XON, 1Y2C
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design., Card GL, Blasdel L, England BP, Zhang C, Suzuki Y, Gillette S, Fong D, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY, Nat Biotechnol 2005 Feb;23(2):201-7. Epub 2005 Jan 30. PMID:15685167
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (1y2d.pdb1.gz) 61 Kb
  • Biological Unit Coordinates (1y2d.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1Y2D
  • CSU: Contacts of Structural Units for 1Y2D
  • Likely Quarternary Molecular Structure file(s) for 1Y2D
  • Structure Factors (634 Kb)
  • Retrieve 1Y2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y2D from S2C, [Save to disk]
  • Re-refined 1y2d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y2D 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 1Y2D
  • 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 1Y2D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y2d_B] [1y2d] [1y2d_A]
  • SWISS-PROT database: [Q08499]
  • Domain organization of [PDE4D_HUMAN] by SWISSPFAM
  • Domain found in 1Y2D: [HDc ] by SMART
  • Other resources with information on 1Y2D
  • Community annotation for 1Y2D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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