4EDZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

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

Date :   27 Mar 12 (Deposition) - 16 May 12 (Release) - 02 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

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, C, D
	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	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	0O5	4	Ligand/Ion	4-(3-METHYLISOQUINOLIN-1-YL)-N-[2-(MORPHOLIN-4-YL)ETHYL]BENZAMIDE
2	GSH	4	Ligand/Ion	GLUTATHIONE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	0O5	2	Ligand/Ion	4-(3-METHYLISOQUINOLIN-1-YL)-N-[2-(MORPHOLIN-4-YL)ETHYL]BENZAMIDE
2	GSH	2	Ligand/Ion	GLUTATHIONE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	0O5	2	Ligand/Ion	4-(3-METHYLISOQUINOLIN-1-YL)-N-[2-(MORPHOLIN-4-YL)ETHYL]BENZAMIDE
2	GSH	2	Ligand/Ion	GLUTATHIONE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	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 , HOH A:303 , HOH A:304 , HOH A:321 , HOH A:360 , HOH A:405 , HOH A:414 , ASP B:97	BINDING SITE FOR RESIDUE GSH A 201
02	AC2	SOFTWARE	MET A:11 , GLY A:13 , ARG A:14 , GLN A:36 , ASP A:96 , MET A:99 , TRP A:104 , TYR A:152 , ILE A:155 , LEU A:199 , HOH A:319 , HOH A:378	BINDING SITE FOR RESIDUE 0O5 A 202
03	AC3	SOFTWARE	HOH A:301 , HOH A:302 , HOH B:301 , HOH B:302	BINDING SITE FOR RESIDUE MG B 201
04	AC4	SOFTWARE	ASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , PRO B:52 , GLN B:63 , SER B:64 , 0O5 B:203 , HOH B:308 , HOH B:312 , HOH B:353 , HOH B:371	BINDING SITE FOR RESIDUE GSH B 202
05	AC5	SOFTWARE	PHE B:9 , MET B:11 , GLY B:13 , ARG B:14 , GLN B:36 , ASP B:96 , MET B:99 , SER B:100 , TRP B:104 , TYR B:152 , ILE B:155 , LEU B:199 , GSH B:202 , HOH B:321	BINDING SITE FOR RESIDUE 0O5 B 203
06	AC6	SOFTWARE	HOH C:301 , HOH C:302 , HOH C:303 , HOH D:2501 , HOH D:2502 , HOH D:2503	BINDING SITE FOR RESIDUE MG C 201
07	AC7	SOFTWARE	TYR C:8 , ARG C:14 , TRP C:39 , LYS C:43 , LYS C:50 , ILE C:51 , GLN C:63 , SER C:64 , HOH C:332 , HOH C:340 , HOH C:351 , ASP D:97	BINDING SITE FOR RESIDUE GSH C 202
08	AC8	SOFTWARE	GLY C:13 , ARG C:14 , GLN C:36 , ASP C:96 , MET C:99 , SER C:100 , TRP C:104 , TYR C:152 , ILE C:155 , LEU C:199 , HOH C:346 , HOH C:391	BINDING SITE FOR RESIDUE 0O5 C 203
09	AC9	SOFTWARE	ASP C:97 , TYR D:8 , ARG D:14 , TRP D:39 , LYS D:43 , LYS D:50 , ILE D:51 , GLN D:63 , SER D:64 , 0O5 D:202 , HOH D:2504 , HOH D:2505 , HOH D:2523 , HOH D:2544 , HOH D:2586 , HOH D:2616	BINDING SITE FOR RESIDUE GSH D 201
10	BC1	SOFTWARE	TYR D:8 , PHE D:9 , MET D:11 , GLY D:13 , ARG D:14 , GLN D:36 , ASP D:96 , MET D:99 , TRP D:104 , TYR D:152 , ILE D:155 , GSH D:201 , HOH D:2520 , HOH D:2592	BINDING SITE FOR RESIDUE 0O5 D 202

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

Asymmetric Unit

No.	Residues
1	Ile A:51	-	Pro A:52
2	Ile B:51	-	Pro B:52
3	Ile C:51	-	Pro C:52
4	Ile D:51	-	Pro D:52

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

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

(no "Exon" information available for 4EDZ)

Asymmetric 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 d4edza1 A:2-75 automated matches                                          d4edza2 A:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeee...hhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4edz 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 d4edzb1 B:1-75 automated matches                                           d4edzb2 B:76-199 automated matches                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh......eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edz B   1 APNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    10        20        30        40        50        60        70        80        90       100     ||112       122       132       142       152       162       172       182       192       
                                                                                                                                   106|                                                                                          
                                                                                                                                    109

Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4edzc1 C:2-75 automated matches                                          d4edzc2 C:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4edz C   2 PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191

Chain D from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains d4edzd1 D:1-75 automated matches                                           d4edzd2 D:76-199 automated matches                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhh........eeee..eeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4edz D   1 APNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKIPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSCFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADFYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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 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	d4edza2	A:76-199
1b	d4edzb2	B:76-199
1c	d4edzc2	C:76-199
1d	d4edzd2	D: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	d4edza1	A:2-75
2b	d4edzb1	B:1-75
2c	d4edzc1	C:2-75
2d	d4edzd1	D:1-75

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:51 - Pro A:52	[ RasMol ]
		Ile B:51 - Pro B:52	[ RasMol ]
		Ile C:51 - Pro C:52	[ RasMol ]
		Ile D:51 - Pro D:52	[ RasMol ]

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	4edz
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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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