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GSTM1_RAT_2_218

Glutathione S-transferase Mu 1 [GST superfamily. Mu family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (GSTM1_RAT):D: GST N-terminal (7, 8, 10, 12, 13, 35, 43, 46, 50, 59:61, 72, 73)
R: Glutathione binding (7, 8)
R: Glutathione binding (43, 46)
R: Glutathione binding (59, 60)
R: Glutathione binding (72, 73)
D: GST C-terminal (105, 108, 109, 112, 116, 208)
209, 210, 212
7, 8, 10, 12, 13, 35, 43, 46, 50, 59:61, 72, 73, 105, 108, 109, 112, 116, 208:210, 212
A2 (GSTM1_RAT):D: GST C-terminal (106, 113)106, 113

Full PDB list

1mtc, 2gst, 3fyg, 3gst, 4gst, 5fwg, 5gst, 6gst, 6gsu, 6gsv, 6gsw, 6gsx, 6gsy (redundant Pocketome entry); 1gsb, 1gsc (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
Y
7
W
8
V
1
0
G
1
2
L
1
3
M
3
5
R
4
3
W
4
6
K
5
0
N
5
9
L
6
0
P
6
1
Q
7
2
S
7
3
M
1
0
5
R
1
0
8
I
1
1
2
Y
1
1
6
I
2
0
8
F
2
0
9
S
2
1
0
D
1
0
6
[1]1mtc.b gpr35 . . . . . . . . . . . . . . . . . F . . . .
[1]2gst.a gps35 . . . . . . . . . . . . . . . . . . . . . .
[1]3fyg.b gpr35 * . . . . . . . . . . . . . . . . . . . . .
[1]3gst.a gpr35 . . . . . . . . . . . . . . . . . . . . . .
[1]4gst.a gtd35 . . . . . . . . . . . . . . . . . . . . . .
[1]5fwg.b gpr35 . * . . . . . * . . . . . . . . . . . . . .
[1]5gst.b gdn32 . . . . . . . . . . . . . . . . . . . . . .
[1]6gst.a gsh20 . . . . . . . . . . . . . . . . . . . . . .
[1]6gsx.a gps35 F . . . . . . . . . . . . . . . . . . . . .
[1]6gsy.a gsh20 F . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 A2
Y
7
W
8
V
1
0
G
1
2
L
1
3
M
3
5
R
4
3
W
4
6
K
5
0
N
5
9
L
6
0
P
6
1
Q
7
2
S
7
3
M
1
0
5
R
1
0
8
M
1
0
9
I
1
1
2
Y
1
1
6
I
2
0
8
F
2
0
9
S
2
1
0
L
2
1
2
D
1
0
6
M
1
1
3
[1]1mtc.b . . . . . . . . . . . . . . . . . . F . . . . . .
[1]2gst.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3fyg.b * . . . . . . . . . . . . . . . . . . . . . . . .
[1]3gst.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gst.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5fwg.b . * . . . . . * . . . . . . . . . . . . . . . . .
[1]5gst.b . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6gst.a . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6gsx.a F . . . . . . . . . . . . . . . . . . . . . . . .
[1]6gsy.a F . . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1mtc.b:gpr
2gst.a:gps
3fyg.b:gpr
3gst.a:gpr
4gst.a:gtd
5fwg.b:gpr
5gst.b:gdn
6gst.a:gsh
6gsx.a:gps
6gsy.a:gsh
[1] 1mtc.b
0.3
0.2 0.7 0.2 0.3 0.2 0.2 0.2 0.3 0.4
[1] 2gst.a 0.4
0
0.3 0.3 0.2 0.1 0.1 0.1 0.1 0.2
[1] 3fyg.b 0.3 0.1
0.1
0.4 0.2 0.2 0.2 0.5 0.2 0.6
[1] 3gst.a 0.2 0 0.6
0
0.1 0.2 0.2 0.1 0 0.1
[1] 4gst.a 0.4 0.3 0.7 0.3
0.2
0.1 0 0.1 0 0.3
[1] 5fwg.b 0.6 0.6 0.6 0.5 0.7
0.4
0.2 0.5 0.4 0.6
[1] 5gst.b 0.6 0.4 0.5 0.5 0.4 0.4
0
0.2 0.5 0.3
[1] 6gst.a 0.4 0.3 0.7 0.4 0.2 0.4 0
0.1
0.3 0.3
[1] 6gsx.a 0.4 0.1 0.4 0.1 0.2 0 0 0.2
0.1
0.3
[1] 6gsy.a 0.8 0.6 0.7 0.5 0.4 0.5 0.2 0.4 0.4
0.4
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1mtc.b
2gst.a
3fyg.b
3gst.a
4gst.a
5fwg.b
5gst.b
6gst.a
6gsx.a
6gsy.a
[1] 1mtc.b
0
.04 .05 .02 .02 .01 .04 .03 .04 .04
[1] 2gst.a .04
0
.05 .03 .02 .04 .02 .03 .02 .03
[1] 3fyg.b .05 .05
0
.06 .06 .06 .05 .08 .05 .07
[1] 3gst.a .02 .03 .06
0
.02 .03 .05 .03 .03 .04
[1] 4gst.a .02 .02 .06 .02
0
.02 .03 .03 .02 .04
[1] 5fwg.b .01 .04 .06 .03 .02
0
.04 .04 .04 .04
[1] 5gst.b .04 .02 .05 .05 .03 .04
0
.04 .03 .05
[1] 6gst.a .03 .03 .08 .03 .03 .04 .04
0
.04 .03
[1] 6gsx.a .04 .02 .05 .03 .02 .04 .03 .04
0
.04
[1] 6gsy.a .04 .03 .07 .04 .04 .04 .05 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1mtc.b
2gst.a
3fyg.b
3gst.a
4gst.a
5fwg.b
5gst.b
6gst.a
6gsx.a
6gsy.a
[1] 1mtc.b
0
0.4 0.9 0.5 0.4 0.5 0.5 0.4 0.4 0.5
[1] 2gst.a 0.4
0
0.9 0.1 0.2 0.5 0.5 0.2 0.2 0.3
[1] 3fyg.b 0.9 0.9
0
0.9 0.9 0.9 0.8 0.9 0.9 0.9
[1] 3gst.a 0.5 0.1 0.9
0
0.2 0.5 0.4 0.2 0.1 0.3
[1] 4gst.a 0.4 0.2 0.9 0.2
0
0.5 0.4 0.2 0.2 0.2
[1] 5fwg.b 0.5 0.5 0.9 0.5 0.5
0
0.4 0.4 0.5 0.5
[1] 5gst.b 0.5 0.5 0.8 0.4 0.4 0.4
0
0.4 0.5 0.5
[1] 6gst.a 0.4 0.2 0.9 0.2 0.2 0.4 0.4
0
0.2 0.3
[1] 6gsx.a 0.4 0.2 0.9 0.1 0.2 0.5 0.5 0.2
0
0.3
[1] 6gsy.a 0.5 0.3 0.9 0.3 0.2 0.5 0.5 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1mtc.b
2gst.a
3fyg.b
3gst.a
4gst.a
5fwg.b
5gst.b
6gst.a
6gsx.a
6gsy.a
[1] 1mtc.b
0
0.7 1.2 0.8 0.7 0.9 0.7 0.7 0.7 0.7
[1] 2gst.a 0.7
0
1.3 0.5 0.4 0.9 0.8 0.4 0.3 0.5
[1] 3fyg.b 1.2 1.3
0
1.3 1.2 1.4 1.3 1.3 1.2 1.3
[1] 3gst.a 0.8 0.5 1.3
0
0.5 0.8 0.8 0.6 0.5 0.7
[1] 4gst.a 0.7 0.4 1.2 0.5
0
0.8 0.8 0.5 0.3 0.6
[1] 5fwg.b 0.9 0.9 1.4 0.8 0.8
0
0.9 0.9 0.8 1.0
[1] 5gst.b 0.7 0.8 1.3 0.8 0.8 0.9
0
0.7 0.8 0.8
[1] 6gst.a 0.7 0.4 1.3 0.6 0.5 0.9 0.7
0
0.4 0.4
[1] 6gsx.a 0.7 0.3 1.2 0.5 0.3 0.8 0.8 0.4
0
0.5
[1] 6gsy.a 0.7 0.5 1.3 0.7 0.6 1.0 0.8 0.4 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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