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1OYJ
Asym. Unit
Info
Asym.Unit (172 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (84 KB)
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(1)
Title
:
CRYSTAL STRUCTURE SOLUTION OF RICE GST1 (OSGSTU1) IN COMPLEX WITH GLUTATHIONE.
Authors
:
D. P. Dixon, A. G. Mcewen, A. J. Lapthorn, R. Edwards
Date
:
04 Apr 03 (Deposition) - 01 Jul 03 (Release) - 25 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Herbicide Detoxification, Plant Glutathione S-Transferase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. P. Dixon, A. G. Mcewen, A. J. Lapthorn, R. Edwards
Forced Evolution Of A Herbicide Detoxifying Glutathione Transferase.
J. Biol. Chem. V. 278 23930 2003
[
close entry info
]
Hetero Components
(4, 39)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
1m: CHLORIDE ION (CLm)
1n: CHLORIDE ION (CLn)
1o: CHLORIDE ION (CLo)
1p: CHLORIDE ION (CLp)
1q: CHLORIDE ION (CLq)
1r: CHLORIDE ION (CLr)
1s: CHLORIDE ION (CLs)
1t: CHLORIDE ION (CLt)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: GLUTATHIONE (GSHa)
3b: GLUTATHIONE (GSHb)
3c: GLUTATHIONE (GSHc)
3d: GLUTATHIONE (GSHd)
3e: GLUTATHIONE (GSHe)
3f: GLUTATHIONE (GSHf)
3g: GLUTATHIONE (GSHg)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
20
Ligand/Ion
CHLORIDE ION
2
GOL
9
Ligand/Ion
GLYCEROL
3
GSH
7
Ligand/Ion
GLUTATHIONE
4
MG
3
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(39, 39)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GSH A:800 , ASP D:205 , HOH D:838 , HOH D:842 , HOH D:853 , HOH D:854
BINDING SITE FOR RESIDUE MG A 815
02
AC2
SOFTWARE
ASP B:205 , GSH C:803 , HOH C:843 , HOH C:867 , HOH C:888 , HOH C:963
BINDING SITE FOR RESIDUE MG C 816
03
AC3
SOFTWARE
HOH A:904 , HOH A:915 , HOH A:927 , HOH A:950 , HOH A:968 , HOH A:969
BINDING SITE FOR RESIDUE MG A 817
04
AC4
SOFTWARE
LYS A:114 , GSH A:800
BINDING SITE FOR RESIDUE CL D 819
05
AC5
SOFTWARE
LYS B:42 , ARG B:54
BINDING SITE FOR RESIDUE CL B 820
06
AC6
SOFTWARE
ARG A:135 , SER D:213 , LYS D:216
BINDING SITE FOR RESIDUE CL D 821
07
AC7
SOFTWARE
GLU C:3 , PHE C:80 , PRO C:81 , GLY C:82
BINDING SITE FOR RESIDUE CL C 822
08
AC8
SOFTWARE
PHE A:80 , GLY A:82
BINDING SITE FOR RESIDUE CL A 823
09
AC9
SOFTWARE
LYS C:114 , GSH C:803
BINDING SITE FOR RESIDUE CL C 824
10
BC1
SOFTWARE
ASP A:44 , LEU A:45
BINDING SITE FOR RESIDUE CL A 825
11
BC2
SOFTWARE
LEU A:125 , LYS A:126
BINDING SITE FOR RESIDUE CL A 826
12
BC3
SOFTWARE
GLU A:152 , PHE A:153
BINDING SITE FOR RESIDUE CL A 827
13
BC4
SOFTWARE
ASP C:205
BINDING SITE FOR RESIDUE CL C 828
14
BC5
SOFTWARE
ARG C:113 , LYS D:55 , GSH D:805
BINDING SITE FOR RESIDUE CL C 829
15
BC6
SOFTWARE
VAL C:66 , SER C:67 , GOL C:813 , ALA D:102 , PHE D:106 , HOH D:967
BINDING SITE FOR RESIDUE CL C 830
16
BC7
SOFTWARE
GLU B:152 , PHE B:153 , GLY B:155 , GLY B:156 , GLY B:157
BINDING SITE FOR RESIDUE CL B 831
17
BC8
SOFTWARE
GLU D:152 , PHE D:153 , GLY D:157 , GLY D:158
BINDING SITE FOR RESIDUE CL D 832
18
BC9
SOFTWARE
SER B:213 , LYS B:216 , ARG C:135
BINDING SITE FOR RESIDUE CL C 833
19
CC1
SOFTWARE
ARG B:54 , ILE D:204 , ASP D:205
BINDING SITE FOR RESIDUE CL D 834
20
CC2
SOFTWARE
HOH A:953
BINDING SITE FOR RESIDUE CL B 835
21
CC3
SOFTWARE
PHE A:185 , SER A:186 , GLU A:189
BINDING SITE FOR RESIDUE CL A 836
22
CC4
SOFTWARE
TRP A:13
BINDING SITE FOR RESIDUE CL A 837
23
CC5
SOFTWARE
ARG D:203
BINDING SITE FOR RESIDUE CL A 838
24
CC6
SOFTWARE
SER A:15 , PHE A:17 , LYS A:42 , LYS A:55 , ILE A:56 , PRO A:57 , GLU A:68 , SER A:69 , HOH A:843 , HOH A:844 , HOH A:884 , HOH A:923 , ARG B:113 , HOH B:845
BINDING SITE FOR RESIDUE GSH A 799
25
CC7
SOFTWARE
LYS A:114 , CYS A:118 , ARG A:121 , GLU A:136 , MG A:815 , HOH A:849 , HOH A:850 , ASP D:205 , CL D:819 , HOH D:838 , HOH D:842 , HOH D:853
BINDING SITE FOR RESIDUE GSH A 800
26
CC8
SOFTWARE
ARG A:113 , SER B:15 , PHE B:17 , LYS B:42 , LYS B:55 , ILE B:56 , PRO B:57 , GLU B:68 , SER B:69 , HOH B:839 , HOH B:848 , HOH B:868 , HOH B:871 , HOH B:892
BINDING SITE FOR RESIDUE GSH B 801
27
CC9
SOFTWARE
SER C:15 , PHE C:17 , LYS C:42 , LYS C:55 , ILE C:56 , PRO C:57 , GLU C:68 , SER C:69 , HOH C:857 , HOH C:863 , HOH C:877 , HOH C:894 , HOH C:965 , HOH C:966 , ARG D:113
BINDING SITE FOR RESIDUE GSH C 802
28
DC1
SOFTWARE
ASP B:205 , ARG C:113 , LYS C:114 , CYS C:118 , ARG C:121 , GLU C:136 , MG C:816 , CL C:824 , HOH C:839 , HOH C:843 , HOH C:864 , HOH C:901 , HOH C:963 , HOH C:1011
BINDING SITE FOR RESIDUE GSH C 803
29
DC2
SOFTWARE
GLN C:130 , ARG C:181 , CYS C:182 , GLY C:183 , GLY C:184 , TYR C:218
BINDING SITE FOR RESIDUE GSH C 804
30
DC3
SOFTWARE
ARG C:113 , CL C:829 , SER D:15 , PHE D:17 , LYS D:42 , LYS D:55 , ILE D:56 , PRO D:57 , GLU D:68 , SER D:69 , HOH D:850 , HOH D:900 , HOH D:930
BINDING SITE FOR RESIDUE GSH D 805
31
DC4
SOFTWARE
THR A:103 , PHE A:106 , HOH A:949 , SER B:49 , PRO B:65 , SER B:67 , HOH B:886
BINDING SITE FOR RESIDUE GOL B 806
32
DC5
SOFTWARE
GLU D:31 , PHE D:32 , LYS D:209 , HIS D:210 , HOH D:852 , HOH D:858
BINDING SITE FOR RESIDUE GOL D 807
33
DC6
SOFTWARE
PHE B:32 , LYS B:209 , HIS B:210 , HOH C:845 , HOH C:890
BINDING SITE FOR RESIDUE GOL C 808
34
DC7
SOFTWARE
TRP C:107 , SER D:49 , ASN D:50 , PRO D:65 , SER D:67 , HOH D:835 , HOH D:921 , HOH D:963
BINDING SITE FOR RESIDUE GOL D 809
35
DC8
SOFTWARE
THR C:173 , ALA C:174 , GLY C:202 , PRO C:212 , SER C:213 , PRO C:214 , HOH C:912
BINDING SITE FOR RESIDUE GOL C 810
36
DC9
SOFTWARE
PHE A:176 , GLU A:180 , ALA A:195 , HOH A:907 , HOH A:970
BINDING SITE FOR RESIDUE GOL A 811
37
EC1
SOFTWARE
PHE A:32 , GLU A:33 , TYR A:34 , TRP C:13 , LYS C:216
BINDING SITE FOR RESIDUE GOL C 812
38
EC2
SOFTWARE
SER C:49 , PRO C:65 , SER C:67 , CL C:830 , HOH C:1041 , PHE D:106
BINDING SITE FOR RESIDUE GOL C 813
39
EC3
SOFTWARE
PRO A:65 , VAL A:66 , SER A:67 , HOH A:955 , TYR B:99 , THR B:103 , PHE B:106
BINDING SITE FOR RESIDUE GOL A 814
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: GST_NTER (A:5-84,B:5-84,C:5-84,D:5-84,A:5-84...)
2: GST_CTER (A:97-220,B:97-220,C:97-220,D:97-22...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GST_NTER
PS50404
Soluble glutathione S-transferase N-terminal domain profile.
GSTU1_ORYSI
5-84
4
A:5-84
B:5-84
C:5-84
D:5-84
GSTU1_ORYSJ
5-84
4
A:5-84
B:5-84
C:5-84
D:5-84
2
GST_CTER
PS50405
Soluble glutathione S-transferase C-terminal domain profile.
GSTU1_ORYSI
97-220
4
A:97-220
B:97-220
C:97-220
D:97-220
GSTU1_ORYSJ
97-220
4
A:97-220
B:97-220
C:97-220
D:97-220
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1oyja1 (A:86-230)
1b: SCOP_d1oyjb1 (B:86-227)
1c: SCOP_d1oyjc1 (C:86-229)
1d: SCOP_d1oyjd1 (D:86-227)
2a: SCOP_d1oyja2 (A:2-85)
2b: SCOP_d1oyjb2 (B:3-85)
2c: SCOP_d1oyjc2 (C:3-85)
2d: SCOP_d1oyjd2 (D:3-85)
View:
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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 tau GST
(2)
Rice (Oryza sativa) [TaxId: 4530]
(1)
1a
d1oyja1
A:86-230
1b
d1oyjb1
B:86-227
1c
d1oyjc1
C:86-229
1d
d1oyjd1
D:86-227
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 tau GST
(2)
Rice (Oryza sativa) [TaxId: 4530]
(1)
2a
d1oyja2
A:2-85
2b
d1oyjb2
B:3-85
2c
d1oyjc2
C:3-85
2d
d1oyjd2
D:3-85
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1oyjA01 (A:2-93)
1b: CATH_1oyjC01 (C:3-94)
1c: CATH_1oyjB01 (B:3-94)
1d: CATH_1oyjD01 (D:3-92)
2a: CATH_1oyjB02 (B:95-227)
2b: CATH_1oyjD02 (D:95-227)
2c: CATH_1oyjC02 (C:95-229)
2d: CATH_1oyjA02 (A:95-230)
View:
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Classes
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Architectures
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
Rice (Oryza sativa)
(2)
1a
1oyjA01
A:2-93
1b
1oyjC01
C:3-94
1c
1oyjB01
B:3-94
1d
1oyjD01
D:3-92
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)
Rice (Oryza sativa)
(1)
2a
1oyjB02
B:95-227
2b
1oyjD02
D:95-227
2c
1oyjC02
C:95-229
2d
1oyjA02
A:95-230
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_GST_C_2_1oyjD01 (D:96-200)
1b: PFAM_GST_C_2_1oyjD02 (D:96-200)
1c: PFAM_GST_C_2_1oyjD03 (D:96-200)
1d: PFAM_GST_C_2_1oyjD04 (D:96-200)
2a: PFAM_GST_N_3_1oyjD05 (D:9-84)
2b: PFAM_GST_N_3_1oyjD06 (D:9-84)
2c: PFAM_GST_N_3_1oyjD07 (D:9-84)
2d: PFAM_GST_N_3_1oyjD08 (D:9-84)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
GST_C
(118)
Family
:
GST_C_2
(16)
Oryza sativa subsp. japonica (Rice)
(1)
1a
GST_C_2-1oyjD01
D:96-200
1b
GST_C_2-1oyjD02
D:96-200
1c
GST_C_2-1oyjD03
D:96-200
1d
GST_C_2-1oyjD04
D:96-200
Clan
:
Thioredoxin
(367)
Family
:
GST_N_3
(20)
Oryza sativa subsp. japonica (Rice)
(1)
2a
GST_N_3-1oyjD05
D:9-84
2b
GST_N_3-1oyjD06
D:9-84
2c
GST_N_3-1oyjD07
D:9-84
2d
GST_N_3-1oyjD08
D:9-84
[
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