5B25	Hydrolase Hydrolase Inhibitor	date	Jan 07, 2016
title	Crystal Structure Of Human Pde1b With Inhibitor 3
authors	K.Ida, W.Lane, G.Snell, S.Sogabe
compound		source
Molecule: Calciumcalmodulin-Dependent 3',5'-Cyclic Nucleot Phosphodiesterase 1b; Chain: A, B, C, D Fragment: Unp Residues 146-506 Synonym: Cam-Pde 1b Ec: 3.1.4.17 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pde1b, Pde1b1, Pdes1b Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pe-Sumopro Amp
symmetry	Space Group: P 43 21 2	R_factor 0.172 R_Free 0.203
crystal cell	length a length b length c angle alpha angle beta angle gamma 102.875 102.875 294.848 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	4QJ, GOL, MG, SO4, ZN	enzyme	Hydrolase E.C.3.1.4.17 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Discovery of Potent and Selective Inhibitors of Phosphodiesterase 1 for the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases., Li P, Zheng H, Zhao J, Zhang L, Yao W, Zhu H, Beard JD, Ida K, Lane W, Snell G, Sogabe S, Heyser CJ, Snyder GL, Hendrick JP, Vanover KE, Davis RE, Wennogle LP, J Med Chem. 2016 Feb 2. PMID:26789933

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (460 Kb) [Save to disk] Biological Unit Coordinates (5b25.pdb1.gz) 116 Kb Biological Unit Coordinates (5b25.pdb2.gz) 116 Kb Biological Unit Coordinates (5b25.pdb3.gz) 117 Kb Biological Unit Coordinates (5b25.pdb4.gz) 117 Kb LPC: Ligand-Protein Contacts for 5B25 CSU: Contacts of Structural Units for 5B25 Structure Factors (2164 Kb) Retrieve 5B25 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5B25 from S2C, [Save to disk] Re-refined 5b25 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5B25 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 5B25

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: [5b25] [5b25_D] [5b25_B] [5b25_A] [5b25_C] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5B25: [HDc ] by SMART

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