3DYN	Hydrolase	date	Jul 28, 2008
title	Human Phosphodiestrase 9 In Complex With Cgmp (Zn Inhibited)
authors	S.Liu, M.N.Mansour, K.Dillman, J.Perez, D.Danley, F.Menniti
compound		source
Molecule: High Affinity Cgmp-Specific 3',5'-Cyclic Phosphod 9a; 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 0.180 R_Free 0.203
crystal cell	length a length b length c angle alpha angle beta angle gamma 103.857 103.857 270.118 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	IBM, MG, PCG, ZN 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] (123 Kb) [Save to disk] Biological Unit Coordinates (3dyn.pdb1.gz) 60 Kb Biological Unit Coordinates (3dyn.pdb2.gz) 60 Kb LPC: Ligand-Protein Contacts for 3DYN CSU: Contacts of Structural Units for 3DYN Likely Quarternary Molecular Structure file(s) for 3DYN Structure Factors (656 Kb) Retrieve 3DYN in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DYN from S2C, [Save to disk] Re-refined 3dyn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DYN 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 3DYN

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 3DYN, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dyn_B] [3dyn_A] [3dyn] SWISS-PROT database: [O76083] Domain organization of [PDE9A_HUMAN] by SWISSPFAM Domain found in 3DYN: [HDc ] by SMART

Other resources with information on 3DYN

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

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