1PD2	Ligase	date	Dec 14, 1998
title	Crystal Structure Of Hematopoietic Prostaglandin D Synthase With Glutathione
authors	M.Miyano, H.Ago
compound		source
Molecule: Hematopoietic Prostaglandin D Synthase Chain: 1, 2 Synonym: Hpgds, Spleen Type Pgds, Glutathione Dependent Pgd Ec: 5.3.99.2 Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Organ: Spleen Cellular_location: Cytoplasm Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21 Expression_system_variant: De3 Expression_system_cellular_location: Cytoplasmic Expression_system_vector: Pt7-7 Expression_system_gene: De3
symmetry	Space Group: P 31 2 1	R_factor 0.204 R_Free 0.289
crystal cell	length a length b length c angle alpha angle beta angle gamma 56.500 56.500 233.400 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	GSH	enzyme	Isomerase E.C.5.3.99.2 BRENDA
related structures	by homologous chain: 1V40
Gene Ontology	Chain Function Process Component 1, 2
Primary reference	Cloning and crystal structure of hematopoietic prostaglandin D synthase., Kanaoka Y, Ago H, Inagaki E, Nanayama T, Miyano M, Kikuno R, Fujii Y, Eguchi N, Toh H, Urade Y, Hayaishi O, Cell 1997 Sep 19;90(6):1085-95. PMID:9323136

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk] Biological Unit Coordinates (1pd2.pdb1.gz) 85 Kb LPC: Ligand-Protein Contacts for 1PD2 CSU: Contacts of Structural Units for 1PD2 Likely Quarternary Molecular Structure file(s) for 1PD2 Structure Factors (193 Kb) Retrieve 1PD2 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1PD2 from S2C, [Save to disk] Re-refined 1pd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1PD2 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 1PD2

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 1PD2, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1pd212, region 1:1-75 [Jmol] [rasmolscript] [script source]     - Domain d1pd211, region 1:76-199 [Jmol] [rasmolscript] [script source]     - Domain d1pd222, region 2:1-75 [Jmol] [rasmolscript] [script source]     - Domain d1pd221, region 2:76-199 [Jmol] [rasmolscript] [script source]     - Domain d1h1pd2, region D:310-432 [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1pd2_1] [1pd2_2] [1pd2] SWISS-PROT database: [O35543] Domain organization of [HPGDS_RAT] by SWISSPFAM

Other resources with information on 1PD2

Community annotation for 1PD2 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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