1Y6E - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

Title :   ORTHORHOMBIC GLUTATHIONE S-TRANSFERASE OF SCHISTOSOMA JAPONICUM

Authors :   A. C. Rufer, L. Thiebach, K. Baer, H. W. Klein, M. Hennig

Date :   06 Dec 04 (Deposition) - 08 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Dimer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. C. Rufer, L. Thiebach, K. Baer, H. W. Klein, M. Hennig
X-Ray Structure Of Glutathione S-Transferase From Schistosoma Japonicum In A New Crystal Form Reveals Flexibility Of The Substrate-Binding Site
Acta Crystallogr. , Sect. F V. 61 263 2005
PubMed-ID: 16511012 | Reference-DOI: 10.1107/S1744309105004823
(for further references see the PDB file header)

Molecule 1 - GLUTATHIONE S-TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.5.1.18
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PAC-G2T
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SCHISTOSOMA JAPONICUM
	Organism Taxid	:	6182

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1Y6E)

(no "Site" information available for 1Y6E)

(no "SS Bond" information available for 1Y6E)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:54	-	Pro A:55
2	Trp A:200	-	Pro A:201
3	Leu B:54	-	Pro B:55
4	Trp B:200	-	Pro B:201

(no "SAP(SNP)/Variant" information available for 1Y6E)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GST26_SCHJA	85-203	2	A:84-202 B:84-202

(no "Exon" information available for 1Y6E)

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:216
 aligned with GST26_SCHJA | P08515 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
          GST26_SCHJA     2 SPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPP 217
               SCOP domains d1y6ea2 A:1-79 automated matches                                               d1y6ea1 A:80-216 automated matches                                                                                                        SCOP domains
               CATH domains 1y6eA01 A:1-80,A:186-212 Glutaredoxin                                           1y6eA02 A:81-185  [code=1.20.1050.10, no name defined]                                                   1y6eA01 A:1-80,A:186-212   ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhh....eeeee...hhhhhhhhh...........eee....eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------GST_CTER  PDB: A:84-202 UniProt: 85-203                                                                                -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y6e A   1 SPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with GST26_SCHJA | P08515 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
          GST26_SCHJA     2 SPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPP 217
               SCOP domains d1y6eb2 B:1-79 automated matches                                               d1y6eb1 B:80-216 automated matches                                                                                                        SCOP domains
               CATH domains 1y6eB01 B:1-80,B:186-212 Glutaredoxin                                           1y6eB02 B:81-185  [code=1.20.1050.10, no name defined]                                                   1y6eB01 B:1-80,B:186-212   ---- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------GST_C-1y6eB01 B:73-186                                                                                            ------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------GST_C-1y6eB02 B:73-186                                                                                            ------------------------------ Pfam domains (2)
           Pfam domains (3) -GST_N-1y6eB03 B:2-76                                                       -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -GST_N-1y6eB04 B:2-76                                                       -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee.....hhhhhhhhhhh....eeeee...hhhhhhhhh...........eee....eeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------GST_CTER  PDB: B:84-202 UniProt: 85-203                                                                                -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y6e B   1 SPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPP 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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)

Schistosoma japonicum [TaxId: 6182] (2)

1a	d1y6ea1	A:80-216
1b	d1y6eb1	B:80-216

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)

Schistosoma japonicum [TaxId: 6182] (3)

2a	d1y6ea2	A:1-79
2b	d1y6eb2	B:1-79

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Schistosoma japonicum. Organism_taxid: 6182. (9)

1a	1y6eA01	A:1-80,A:186-212
1b	1y6eB01	B:1-80,B:186-212

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 (267)

Homologous Superfamily: [code=1.20.1050.10, no name defined] (249)

Schistosoma japonicum. Organism_taxid: 6182. (9)

2a	1y6eA02	A:81-185
2b	1y6eB02	B:81-185

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GST_C (118)

Family: GST_C (102)

Schistosoma japonicum (Blood fluke) (8)

1a	GST_C-1y6eB01	B:73-186
1b	GST_C-1y6eB02	B:73-186

Clan: Thioredoxin (367)

Family: GST_N (88)

Schistosoma japonicum (Blood fluke) (8)

2a	GST_N-1y6eB03	B:2-76
2b	GST_N-1y6eB04	B:2-76

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GST26_SCHJA | P08515)

molecular function
	GO:0004364		glutathione transferase activity		Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group.
	GO:0016740		transferase activity		Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

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
(no "Ligands, Modified Residues, Ions" information available for 1y6e)

	Sites
(no "Sites" information available for 1y6e)

	Cis Peptide Bonds
		Leu A:54 - Pro A:55	[ RasMol ]
		Leu B:54 - Pro B:55	[ RasMol ]
		Trp A:200 - Pro A:201	[ RasMol ]
		Trp B:200 - Pro B:201	[ 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 ](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
	1y6e
		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
	GST26_SCHJA \| P08515
		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

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
	GST26_SCHJA \| P08515
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1Y6E)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (2, 2)

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