1BYE - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   GLUTATHIONE S-TRANSFERASE I FROM MAIS IN COMPLEX WITH ATRAZINE GLUTATHIONE CONJUGATE

Authors :   L. Prade, R. Huber, B. Bieseler

Date :   14 Oct 98 (Deposition) - 21 Oct 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A (2x),B (2x),C (2x),D (2x)
Biol. Unit 4: A (1x),B (1x),C (1x),D (1x)

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

Reference :   L. Prade, R. Huber, B. Bieseler
Structures Of Herbicides In Complex With Their Detoxifying Enzyme Glutathione S-Transferase - Explanations For The Selectivity Of The Enzyme In Plants.
Structure V. 6 1445 1998
PubMed-ID: 9817846 | Reference-DOI: 10.1016/S0969-2126(98)00143-9
(for further references see the PDB file header)

Molecule 1 - PROTEIN (GLUTATHIONE S-TRANSFERASE)
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ZEA MAYS
	Organism Taxid	:	4577

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ATA	4	Ligand/Ion	ATRAZINE GLUTATHIONE CONJUGATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ATA	2	Ligand/Ion	ATRAZINE GLUTATHIONE CONJUGATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ATA	2	Ligand/Ion	ATRAZINE GLUTATHIONE CONJUGATE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	ATA	4	Ligand/Ion	ATRAZINE GLUTATHIONE CONJUGATE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	ATA	2	Ligand/Ion	ATRAZINE GLUTATHIONE CONJUGATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:10 , SER A:11 , TRP A:12 , ASN A:13 , ASN A:34 , PHE A:35 , ALA A:36 , HIS A:40 , GLY A:52 , GLN A:53 , VAL A:54 , PRO A:55 , GLU A:66 , SER A:67 , ILE A:118 , MET A:121 , HOH A:1002	BINDING SITE FOR RESIDUE ATA A 1001
2	AC2	SOFTWARE	HOH A:1005 , MET B:10 , SER B:11 , ASN B:13 , PHE B:35 , LYS B:41 , GLY B:52 , GLN B:53 , VAL B:54 , GLU B:66 , SER B:67 , ILE B:118 , MET D:121 , LEU D:122 , GLY D:123	BINDING SITE FOR RESIDUE ATA B 1002
3	AC3	SOFTWARE	SER C:11 , ASN C:13 , PHE C:35 , GLN C:53 , VAL C:54 , PRO C:55 , GLU C:66 , SER C:67 , ILE C:118 , HOH C:1017	BINDING SITE FOR RESIDUE ATA C 1003
4	AC4	SOFTWARE	MET B:121 , LEU B:122 , ASN C:103 , MET D:10 , SER D:11 , ASN D:13 , PHE D:35 , HIS D:40 , LYS D:41 , GLN D:53 , VAL D:54 , PRO D:55 , GLU D:66 , SER D:67 , ILE D:118 , HOH D:1006	BINDING SITE FOR RESIDUE ATA D 1004

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

Asymmetric Unit

No.	Residues
1	Val A:54	-	Pro A:55
2	Val B:54	-	Pro B:55
3	Val D:54	-	Pro D:55

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_NTER	PS50404	Soluble glutathione S-transferase N-terminal domain profile.	GSTF1_MAIZE	2-83	4	A:1-82 B:1-82 C:1-82 D:1-82
2	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTF1_MAIZE	88-214	4	A:87-213 B:87-213 C:87-213 D:87-213

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_NTER	PS50404	Soluble glutathione S-transferase N-terminal domain profile.	GSTF1_MAIZE	2-83	2	A:1-82 B:1-82 - -
2	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTF1_MAIZE	88-214	2	A:87-213 B:87-213 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_NTER	PS50404	Soluble glutathione S-transferase N-terminal domain profile.	GSTF1_MAIZE	2-83	2	- - C:1-82 D:1-82
2	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTF1_MAIZE	88-214	2	- - C:87-213 D:87-213

Biological Unit 3 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_NTER	PS50404	Soluble glutathione S-transferase N-terminal domain profile.	GSTF1_MAIZE	2-83	8	A:1-82 B:1-82 C:1-82 D:1-82
2	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTF1_MAIZE	88-214	8	A:87-213 B:87-213 C:87-213 D:87-213

Biological Unit 4 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GST_NTER	PS50404	Soluble glutathione S-transferase N-terminal domain profile.	GSTF1_MAIZE	2-83	4	A:1-82 B:1-82 C:1-82 D:1-82
2	GST_CTER	PS50405	Soluble glutathione S-transferase C-terminal domain profile.	GSTF1_MAIZE	88-214	4	A:87-213 B:87-213 C:87-213 D:87-213

(no "Exon" information available for 1BYE)

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:213
 aligned with GSTF1_MAIZE | P12653 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
          GSTF1_MAIZE     2 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 214
               SCOP domains d1byea2 A:1-80 Class phi GST                                                    d1byea1 A:81-213 Class phi GST                                                                                                        SCOP domains
               CATH domains -1byeA01 A:2-83 Glutaredoxin                                                       1byeA02 A:84-206  [code=1.20.1050.10, no name defined]                                                                     ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhh...........hhh.hhh...hhh...................hhhhhhhhhhhh.hhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh.....hhhh.hhhhhhhhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GST_NTER  PDB: A:1-82 UniProt: 2-83                                               ----GST_CTER  PDB: A:87-213 UniProt: 88-214                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bye A   1 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 213
                                    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:213
 aligned with GSTF1_MAIZE | P12653 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
          GSTF1_MAIZE     2 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 214
               SCOP domains d1byeb2 B:1-80 Class phi GST                                                    d1byeb1 B:81-213 Class phi GST                                                                                                        SCOP domains
               CATH domains -1byeB01 B:2-83 Glutaredoxin                                                       1byeB02 B:84-206  [code=1.20.1050.10, no name defined]                                                                     ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh..............hhh.hhh...........eee..eee..hhhhhhhhhhhh.hhh.......hhhhhhhhhhhhh...hhhhhhhh......hhh.....hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh.hhhhh........hhh..hhhhhhhhhhhh...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GST_NTER  PDB: B:1-82 UniProt: 2-83                                               ----GST_CTER  PDB: B:87-213 UniProt: 88-214                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bye B   1 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with GSTF1_MAIZE | P12653 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
          GSTF1_MAIZE     2 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 214
               SCOP domains d1byec2 C:1-80 Class phi GST                                                    d1byec1 C:81-213 Class phi GST                                                                                                        SCOP domains
               CATH domains -1byeC01 C:2-83 Glutaredoxin                                                       1byeC02 C:84-206  [code=1.20.1050.10, no name defined]                                                                     ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.......hhhhhhhhhhh..................hhhhhh.......eeee..eeee.hhhhhhhhhhhh.hhhh....hhh.....hhhhhhhh...hhhhhhhhhh.hhhh........hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh......hhhh.hhhhhhhhhhhh...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GST_NTER  PDB: C:1-82 UniProt: 2-83                                               ----GST_CTER  PDB: C:87-213 UniProt: 88-214                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bye C   1 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:213
 aligned with GSTF1_MAIZE | P12653 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
          GSTF1_MAIZE     2 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 214
               SCOP domains d1byed2 D:1-80 Class phi GST                                                    d1byed1 D:81-213 Class phi GST                                                                                                        SCOP domains
               CATH domains -1byeD01 D:2-83 Glutaredoxin                                                       1byeD02 D:84-206  [code=1.20.1050.10, no name defined]                                                                     ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..........hhhhhhh....eeee.......hhh.hhhhhh.......eeee..eeee...hhhhh................hhhhhhhh........hhhhhhhhhh...hhhh......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh..hhh.hhh.hhhhhhhhhhhh...hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GST_NTER  PDB: D:1-82 UniProt: 2-83                                               ----GST_CTER  PDB: D:87-213 UniProt: 88-214                                                                                         PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bye D   1 APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNPFGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEVEANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLTKCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERPSVQKVAALMKPSA 213
                                    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 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: Class phi GST (5)

Maize (Zea mays), type I [TaxId: 4577] (2)

1a	d1byea1	A:81-213
1b	d1byeb1	B:81-213
1c	d1byec1	C:81-213
1d	d1byed1	D:81-213

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

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Glutathione S-transferase (GST), N-terminal domain (216)

Protein domain: Class phi GST (5)

Maize (Zea mays), type I [TaxId: 4577] (2)

2a	d1byea2	A:1-80
2b	d1byeb2	B:1-80
2c	d1byec2	C:1-80
2d	d1byed2	D:1-80

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Zea mays. Organism_taxid: 4577. (1)

1a	1byeA01	A:2-83
1b	1byeB01	B:2-83
1c	1byeC01	C:2-83
1d	1byeD01	D:2-83

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)

Zea mays. Organism_taxid: 4577. (1)

2a	1byeA02	A:84-206
2b	1byeB02	B:84-206
2c	1byeC02	C:84-206
2d	1byeD02	D:84-206

(no "Pfam Domain" information available for 1BYE)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GSTF1_MAIZE | P12653)

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 Unit
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	GSTF1_MAIZE \| P12653	:	1axd

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

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