3DYL	Hydrolase	date	Jul 28, 2008
title	Human Phosphdiesterase 9 Substrate Complex (Es Complex)
authors	S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti
compound		source
Molecule: Human Phosphodiesterase 9 Chain: A, B Fragment: Catalytic Domain, Unp Residues 242-566 Ec: 3.1.4.35 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Pde9a Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 41 21 2	R_factor 0.188 R_Free 0.219
crystal cell	length a length b length c angle alpha angle beta angle gamma 103.787 103.787 269.799 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	FMT, IBM, MG, MN, PCG BindingDB	enzyme	Hydrolase E.C.3.1.4.35 BRENDA
Gene Ontology	Chain Function Process Component A, B
Primary reference	Structural basis for the catalytic mechanism of human phosphodiesterase 9., Liu S, Mansour MN, Dillman KS, Perez JR, Danley DE, Aeed PA, Simons SP, Lemotte PK, Menniti FS, Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13309-14. Epub 2008 Aug 29. PMID:18757755

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk] Biological Unit Coordinates (3dyl.pdb1.gz) 56 Kb Biological Unit Coordinates (3dyl.pdb2.gz) 56 Kb LPC: Ligand-Protein Contacts for 3DYL CSU: Contacts of Structural Units for 3DYL Likely Quarternary Molecular Structure file(s) for 3DYL Structure Factors (428 Kb) Retrieve 3DYL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DYL from S2C, [Save to disk] Re-refined 3dyl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DYL 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 3DYL

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 3DYL, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dyl_B] [3dyl_A] [3dyl] SWISS-PROT database: [O76083] Domain organization of [PDE9A_HUMAN] by SWISSPFAM Domain found in 3DYL: [HDc ] by SMART

Other resources with information on 3DYL

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

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