1YDY	Hydrolase	date	Dec 27, 2004
title	Crystal Structure Of Periplasmic Glycerophosphodiester Phosphodiesterase From Escherichia Coli
authors	V.N.Malashkevich, E.Fedorov, S.C.Almo, S.K.Burley, New York Sgx Center For Structural Genomics (Nysgxrc)
compound		source
Molecule: Glycerophosphoryl Diester Phosphodiesterase Chain: A, B Synonym: Glycerophosphodiester Phosphodiesterase Ec: 3.1.4.46 Engineered: Yes		Organism_scientific: Escherichia Coli Organism_taxid: 562 Gene: Glpq Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21
symmetry	Space Group: P 21 21 21	R_factor 0.187 R_Free 0.228
crystal cell	length a length b length c angle alpha angle beta angle gamma 63.789 74.469 157.219 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	CA, GOL	enzyme	Hydrolase E.C.3.1.4.46 BRENDA
related structures	by homologous chain: 1T8Q
Gene Ontology	Chain Function Process Component A, B

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk] Biological Unit Coordinates (1ydy.pdb1.gz) 120 Kb LPC: Ligand-Protein Contacts for 1YDY CSU: Contacts of Structural Units for 1YDY Likely Quarternary Molecular Structure file(s) for 1YDY Structure Factors (1251 Kb) Retrieve 1YDY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1YDY from S2C, [Save to disk] Re-refined 1ydy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1YDY 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 1YDY

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 1YDY, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1ydy_B] [1ydy_A] [1ydy] SWISS-PROT database: [P09394] Domain organization of [GLPQ_ECOLI] by SWISSPFAM

Other resources with information on 1YDY

Community annotation for 1YDY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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