4EDY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HH-PGDS WITH WATER DISPLACING INHIBITOR

Authors :   J. E. Day, A. Thorarensen, J. I. Trujillo, J. R. Kiefer

Date :   27 Mar 12 (Deposition) - 03 Oct 12 (Release) - 02 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym./Biol. Unit : A,B

Keywords :   Inhibitor, Solvent Replacement, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Trujillo, J. R. Kiefer, W. Huang, J. E. Day, J. Moon, G. M. Jerome, C. P. Bono, C. M. Kornmeier, M. L. Williams, C. Kuhn, G. R. Rennie, T. A. Wynn, C. P. Carron, A. Thorarensen
Investigation Of The Binding Pocket Of Human Hematopoietic Prostaglandin (Pg) D2 Synthase (Hh-Pgds): A Tale Of Two Waters.
Bioorg. Med. Chem. Lett. V. 22 3795 2012
PubMed-ID: 22546671 | Reference-DOI: 10.1016/J.BMCL.2012.04.004

Molecule 1 - HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
	Chains	:	A, B
	EC Number	:	5.3.99.2, 2.5.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GSTS, HPGDS, PGDS, PTGDS2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	H-PGDS, GST CLASS-SIGMA, GLUTATHIONE S-TRANSFERASE, GLUTATHIONE-DEPENDENT PGD SYNTHASE, GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE, PROSTAGLANDIN-H2 D-ISOMERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	9PQ	1	Ligand/Ion	4-[2-(HYDROXYMETHYL)NAPHTHALEN-1-YL]-N-[2-(MORPHOLIN-4-YL)ETHYL]BENZAMIDE
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	GSH	2	Ligand/Ion	GLUTATHIONE
4	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:3312 , HOH A:3313 , HOH A:3314 , HOH B:667 , HOH B:668 , HOH B:669	BINDING SITE FOR RESIDUE MG A 201
2	AC2	SOFTWARE	TYR A:8 , ARG A:14 , TRP A:39 , LYS A:43 , LYS A:50 , ILE A:51 , PRO A:52 , GLN A:63 , SER A:64 , 9PQ A:203 , HOH A:3002 , HOH A:3104 , HOH A:3167 , HOH A:3169 , HOH A:3177 , HOH A:3195 , HOH A:3262 , HOH A:3278 , ASP B:97	BINDING SITE FOR RESIDUE GSH A 202
3	AC3	SOFTWARE	TYR A:8 , GLY A:13 , ARG A:14 , GLN A:36 , ASP A:96 , MET A:99 , TRP A:104 , TYR A:152 , THR A:159 , LEU A:199 , GSH A:202 , HOH A:3164 , HOH A:3278	BINDING SITE FOR RESIDUE 9PQ A 203
4	AC4	SOFTWARE	GLY B:13 , MET B:99 , TYR B:152	BINDING SITE FOR RESIDUE DMS B 201
5	AC5	SOFTWARE	ASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , GLN B:63 , SER B:64 , HOH B:309 , HOH B:352 , HOH B:399 , HOH B:430 , HOH B:437 , HOH B:493 , HOH B:628 , HOH B:645	BINDING SITE FOR RESIDUE GSH B 202

(no "SS Bond" information available for 4EDY)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:51	-	Pro A:52
2	Ile B:51	-	Pro B:52

(no "SAP(SNP)/Variant" information available for 4EDY)

(no "PROSITE Motif" information available for 4EDY)

(no "Exon" information available for 4EDY)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4edya1 A:2-75 automated matches                                          d4edya2 A:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4edy A   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d4edyb1 B:1-75 automated matches                                           d4edyb2 B:76-199 automated matches                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh....eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edy B   1 HPNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    10        20        30        40        50        60        70        80        90       100     ||112       122       132       142       152       162       172       182       192       
                                                                                                                                   106|                                                                                          
                                                                                                                                    109

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: GST C-terminal domain-like (353)

Superfamily: GST C-terminal domain-like (353)

Family: Glutathione S-transferase (GST), C-terminal domain (263)

Protein domain: automated matches (50)

Human (Homo sapiens) [TaxId: 9606] (35)

1a	d4edya2	A:76-199
1b	d4edyb2	B:76-199

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Human (Homo sapiens) [TaxId: 9606] (87)

2a	d4edya1	A:2-75
2b	d4edyb1	B:1-75

(no "CATH Domain" information available for 4EDY)

(no "Pfam Domain" information available for 4EDY)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		9PQ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DMS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GSH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:51 - Pro A:52	[ RasMol ]
		Ile B:51 - Pro B:52	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4edy
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HPGDS_HUMAN \| O60760
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.5.1.18
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	5.3.99.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HPGDS_HUMAN \| O60760
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 21)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File