1SOJ Hydrolase date Mar 15, 2004
title Catalytic Domain Of Human Phosphodiesterase 3b In Complex With Ibmx
authors G.Scapin, S.B.Patel, C.Chung, J.P.Varnerin, S.D.Edmondson, A.Mastracchio, E.R.Parmee, J.W.Becker, S.B.Singh, L.H.Van Der Ploeg, M.R.Tota
compound source
Molecule: Cgmp-Inhibited 3',5'-Cyclic Phosphodiesterase B
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Fragment: Catalytic Domain, Residues 654-1073
Synonym: Cyclic Gmp Inhibited Phosphodiesterase B, Cgi-Pde B, Cgipde1, Cgip1;
Ec: 3.1.4.17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde3b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Codonplus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30a
symmetry Space Group: C 1 2 1
R_factor 0.231 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
275.046 147.078 253.485 90.00 109.84 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand IBM, MG BindingDB enzyme Hydrolase E.C.3.1.4.17 BRENDA
related structures by homologous chain: 1SO2
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, K, E, B, H, C, D, I, G, L


Primary referenceCrystal structure of human phosphodiesterase 3B: atomic basis for substrate and inhibitor specificity., Scapin G, Patel SB, Chung C, Varnerin JP, Edmondson SD, Mastracchio A, Parmee ER, Singh SB, Becker JW, Van der Ploeg LH, Tota MR, Biochemistry 2004 May 25;43(20):6091-100. PMID:15147193
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (740 Kb) [Save to disk]
  • Biological Unit Coordinates (1soj.pdb1.gz) 129 Kb
  • Biological Unit Coordinates (1soj.pdb2.gz) 128 Kb
  • Biological Unit Coordinates (1soj.pdb3.gz) 129 Kb
  • Biological Unit Coordinates (1soj.pdb4.gz) 129 Kb
  • Biological Unit Coordinates (1soj.pdb5.gz) 128 Kb
  • Biological Unit Coordinates (1soj.pdb6.gz) 129 Kb
  • LPC: Ligand-Protein Contacts for 1SOJ
  • CSU: Contacts of Structural Units for 1SOJ
  • Likely Quarternary Molecular Structure file(s) for 1SOJ
  • Structure Factors (1803 Kb)
  • Retrieve 1SOJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SOJ from S2C, [Save to disk]
  • Re-refined 1soj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SOJ 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 1SOJ
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1SOJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1soja_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1sojb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1sojc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1sojd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1soje_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1sojf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1sojg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1sojh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1soji_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1sojj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1sojk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1sojl_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1soj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1soj_L] [1soj_G] [1soj_B] [1soj_C] [1soj_H] [1soj_D] [1soj] [1soj_I] [1soj_A] [1soj_J] [1soj_K] [1soj_E] [1soj_F]
  • SWISS-PROT database: [Q13370]
  • Domain organization of [PDE3B_HUMAN] by SWISSPFAM
  • Domain found in 1SOJ: [HDc ] by SMART
  • Other resources with information on 1SOJ
  • Community annotation for 1SOJ 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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