1VF3 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CGSTA1-1 IN COMPLEX WITH GLUTATHIONE CONJUGATE OF CDNB

Authors :   S. C. Lin, Y. C. Lo, M. F. Tam, Y. C. Liaw

Date :   07 Apr 04 (Deposition) - 23 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

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

Reference :   S. C. Lin, Y. C. Lo, M. F. Tam, Y. C. Liaw
Crystal Structures Of Chicken Glutathione S-Transferase A1-1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLUTATHIONE S-TRANSFERASE 3
	Chains	:	A, B
	EC Number	:	2.5.1.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBACE
	Expression System Strain	:	TG1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GTA3
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	GLUTATHIONE S-TRANSFERASE A1-1, GST-CL3, GST CLASS-ALPHA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	GDN	2	Ligand/Ion	GLUTATHIONE S-(2,4 DINITROBENZENE)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:9 , GLY A:14 , LYS A:15 , GLN A:54 , VAL A:55 , GLN A:67 , THR A:68 , LEU A:107 , SER A:108 , PHE A:111 , MET A:222 , TYR A:223 , VAL A:226 , HOH A:4045 , HOH A:4075 , HOH A:4089 , HOH A:4136 , ASP B:1101 , ARG B:1131	BINDING SITE FOR RESIDUE GDN A 2500
2	AC2	SOFTWARE	ASP A:101 , ARG A:131 , TYR B:1009 , LYS B:1015 , GLN B:1054 , VAL B:1055 , GLN B:1067 , THR B:1068 , LEU B:1107 , SER B:1108 , PHE B:1111 , MET B:1222 , TYR B:1223 , HOH B:4042 , HOH B:4148	BINDING SITE FOR RESIDUE GDN B 3600

(no "SS Bond" information available for 1VF3)

Asymmetric/Biological Unit

No.	Residues
1	Val A:55	-	Pro A:56
2	Val B:1055	-	Pro B:1056

Asymmetric/Biological Unit (9, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GSTA3_CHICK_001 *	L	45	V	GSTA3_CHICK	---	---	A B	L	45 1045	V
2	UniProt	VAR_GSTA3_CHICK_002 *	S	47	A	GSTA3_CHICK	---	---	A B	S	47 1047	A
3	UniProt	VAR_GSTA3_CHICK_003 *	I	49	F	GSTA3_CHICK	---	---	A B	I	49 1049	F
4	UniProt	VAR_GSTA3_CHICK_004 *	I	49	V	GSTA3_CHICK	---	---	A B	I	49 1049	V
5	UniProt	VAR_GSTA3_CHICK_005 *	F	52	R	GSTA3_CHICK	---	---	A B	F	52 1052	R
6	UniProt	VAR_GSTA3_CHICK_006 *	W	155	R	GSTA3_CHICK	---	---	A B	W	155 1155	R
7	UniProt	VAR_GSTA3_CHICK_007 *	A	163	T	GSTA3_CHICK	---	---	A B	A	163 1163	T
8	UniProt	VAR_GSTA3_CHICK_008 *	M	166	A	GSTA3_CHICK	---	---	A B	M	166 1166	A
9	UniProt	VAR_GSTA3_CHICK_009 *	E	168	V	GSTA3_CHICK	---	---	A B	E	168 1168	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	GSTA3_CHICK	85-207	2	A:85-207 B:1085-1207

(no "Exon" information available for 1VF3)

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:225
 aligned with GSTA3_CHICK | P26697 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         GSTA3_CHICK      4 KPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQSGILMFQQVPMVEIDGMKLVQTRAILNYIAGKYNLYGKDLKERALIDMYVGGTDDLMGFLLSFPFLSAEDKVKQCAFVVEKATSRYFPAYEKVLKDHGQDFLVGNRLSWADIHLLEAILMVEEKKSDALSGFPLLQAFKKRISSIPTIKKFLAPGSKRKPISDDKYVETVRRVLRMYYDVKP  228
               SCOP domains d1vf3a1 A:4-80 automated matches                                             d1vf3a2 A:81-228 automated matches                                                                                                                   SCOP domains
               CATH domains 1vf3A01 A:4-81,A:191-228 Glutaredoxin                                         1vf3A02 A:82-190  [code=1.20.1050.10, no name defined]                                                       1vf3A01 A:4-81,A:191-228 Glutaredoxin  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh........eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------GST_CTER  PDB: A:85-207 UniProt: 85-207                                                                                    --------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vf3 A    4 KPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQSGILMFQQVPMVEIDGMKLVQTRAILNYIAGKYNLYGKDLKERALIDMYVGGTDDLMGFLLSFPFLSAEDKVKQCAFVVEKATSRYFPAYEKVLKDHGQDFLVGNRLSWADIHLLEAILMVEEKKSDALSGFPLLQAFKKRISSIPTIKKFLAPGSKRKPISDDKYVETVRRVLRMYYDVKP  228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with GSTA3_CHICK | P26697 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
         GSTA3_CHICK      4 KPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQSGILMFQQVPMVEIDGMKLVQTRAILNYIAGKYNLYGKDLKERALIDMYVGGTDDLMGFLLSFPFLSAEDKVKQCAFVVEKATSRYFPAYEKVLKDHGQDFLVGNRLSWADIHLLEAILMVEEKKSDALSGFPLLQAFKKRISSIPTIKKFLAPGSKRKPISDDKYVETVRRVLRMYYDVKP  228
               SCOP domains d1vf3b1 B:1004-1080 automated matches                                        d1vf3b2 B:1081-1228 automated matches                                                                                                                SCOP domains
               CATH domains 1vf3B01 B:1004-1081,B:1191-1228 Glutaredoxin                                  1vf3B02 B:1082-1190  [code=1.20.1050.10, no name defined]                                                    1vf3B01 B:1004-1081,B:1191-1228        CATH domains
           Pfam domains (1) -GST_N-1vf3B03 B:1005-1077                                                ---------------------GST_C-1vf3B01 B:1099-1192                                                                     ------------------------------------ Pfam domains (1)
           Pfam domains (2) -GST_N-1vf3B04 B:1005-1077                                                ---------------------GST_C-1vf3B02 B:1099-1192                                                                     ------------------------------------ Pfam domains (2)
         Sec.struct. author ..eee.......hhhhhhhhhhh....eee...hhhhhhhhhhhh........eeee..eeeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....... Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------V-A-F--R------------------------------------------------------------------------------------------------------R-------T--A-V------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------V----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------------GST_CTER  PDB: B:1085-1207 UniProt: 85-207                                                                                 --------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vf3 B 1004 KPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQSGILMFQQVPMVEIDGMKLVQTRAILNYIAGKYNLYGKDLKERALIDMYVGGTDDLMGFLLSFPFLSAEDKVKQCAFVVEKATSRYFPAYEKVLKDHGQDFLVGNRLSWADIHLLEAILMVEEKKSDALSGFPLLQAFKKRISSIPTIKKFLAPGSKRKPISDDKYVETVRRVLRMYYDVKP 1228
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223

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: automated matches (86)

Protein domain: automated matches (86)

Chicken (Gallus gallus) [TaxId: 9031] (4)

1a	d1vf3a2	A:81-228
1b	d1vf3b2	B:1081-1228

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)

Chicken (Gallus gallus) [TaxId: 9031] (4)

2a	d1vf3a1	A:4-80
2b	d1vf3b1	B:1004-1080

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)

Chicken (Gallus gallus) (6)

1a	1vf3A01	A:4-81,A:191-228
1b	1vf3B01	B:1004-1081,B:1191-1228

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)

Chicken (Gallus gallus) (6)

2a	1vf3A02	A:82-190
2b	1vf3B02	B:1082-1190

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GST_C (118)

Family: GST_C (102)

Gallus gallus (Chicken) (3)

1a	GST_C-1vf3B01	B:1099-1192
1b	GST_C-1vf3B02	B:1099-1192

Clan: Thioredoxin (367)

Family: GST_N (88)

Gallus gallus (Chicken) (3)

2a	GST_N-1vf3B03	B:1005-1077
2b	GST_N-1vf3B04	B:1005-1077

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GSTA3_CHICK | P26697)

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.
biological process
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Val A:55 - Pro A:56	[ RasMol ]
		Val B:1055 - Pro B:1056	[ RasMol ]

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	1vf3
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	GSTA3_CHICK \| P26697
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	2.5.1.18
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UniProtKB/Swiss-Prot
	GSTA3_CHICK \| P26697	:	1vf1 1vf2 1vf4

1vf1	NATIVE CRYSTAL IN COMPLEX WITH GLUTATHIONE
1vf2	CGSTA1-1 IN COMPLEX WITH S-HEXYL GLUTATHIONE
1vf4	CGSTA1-1 APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (9, 18)

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 (5, 5)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File