4EC0 - 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

Date :   26 Mar 12 (Deposition) - 16 May 12 (Release) - 02 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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 (3, 4)

No.	Name	Count	Type	Full Name
1	7PQ	1	Ligand/Ion	4-[2-(AMINOMETHYL)NAPHTHALEN-1-YL]-N-[2-(MORPHOLIN-4-YL)ETHYL]BENZAMIDE
2	GSH	2	Ligand/Ion	GLUTATHIONE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	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 , 7PQ A:203 , HOH A:301 , HOH A:402 , HOH A:464 , HOH A:472 , HOH A:652 , HOH A:684 , ASP B:1097	BINDING SITE FOR RESIDUE GSH A 201
2	AC2	SOFTWARE	HOH A:412 , HOH A:423 , HOH A:459 , HOH B:1372 , HOH B:1384 , HOH B:1437	BINDING SITE FOR RESIDUE MG A 202
3	AC3	SOFTWARE	TYR A:8 , GLY A:13 , ARG A:14 , ASP A:96 , MET A:99 , TRP A:104 , TYR A:152 , THR A:159 , LEU A:199 , GSH A:201 , HOH A:461	BINDING SITE FOR RESIDUE 7PQ A 203
4	AC4	SOFTWARE	ASP A:97 , TYR B:1008 , ARG B:1014 , TRP B:1039 , LYS B:1043 , LYS B:1050 , ILE B:1051 , GLN B:1063 , SER B:1064 , HOH B:1309 , HOH B:1353 , HOH B:1404 , HOH B:1430 , HOH B:1438 , HOH B:1649	BINDING SITE FOR RESIDUE GSH B 1201

(no "SS Bond" information available for 4EC0)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:51	-	Pro A:52
2	Ile B:1051	-	Pro B:1052

(no "SAP(SNP)/Variant" information available for 4EC0)

(no "PROSITE Motif" information available for 4EC0)

(no "Exon" information available for 4EC0)

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:199
                                                                                                                                                                                                                                        
               SCOP domains d4ec0a1 A:1-75 automated matches                                           d4ec0a2 A:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhh...eeee....hhhhhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ec0 A    1 MPNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL  199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                         
               SCOP domains d4ec0b1 B:1000-1075 automated matches                                       d4ec0b2 B:1076-1199 automated matches                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhhhh....eeeeehhhhhhhhhhh.......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ec0 B 1000 HMPNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 1199
                                  1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199

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	d4ec0a2	A:76-199
1b	d4ec0b2	B:1076-1199

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	d4ec0a1	A:1-75
2b	d4ec0b1	B:1000-1075

(no "CATH Domain" information available for 4EC0)

(no "Pfam Domain" information available for 4EC0)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		7PQ	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GSH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:51 - Pro A:52	[ RasMol ]
		Ile B:1051 - Pro B:1052	[ RasMol ]

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	4ec0
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	2.5.1.18
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	5.3.99.2
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		Interatomic Contacts of Structural Units	:	CSU
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

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)

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