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DHAR1_ORYSJ_1_213

Probable glutathione S-transferase DHAR1, cytosolic [GST superfamily. DHAR family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHAR1_ORYSJ):D: GST N-terminal (19:22)
D: GST C-terminal (104, 108, 112, 160, 206, 207, 210)
8
8, 19:22, 104, 108, 112, 160, 206, 207, 210
Metals (Me):Ca

Full PDB list

5d9t, 5d9v, 5d9w, 5d9x

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
K
8
D
1
9
P
2
1
F
1
0
4
T
1
0
8
K
1
1
2
H
1
6
0
G
2
0
6
W
2
0
7
K
2
1
0
[1]5d9t.a none . . . . . . . . . .
[1]5d9v.a none . . . . . . . . . . Ca
[1]5d9w.a asc12 . . . . . . . . . .
[1]5d9x.a gsh20 . . . . . . . . . . Ca

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 Me
K
8
D
1
9
C
2
0
P
2
1
F
2
2
F
1
0
4
T
1
0
8
K
1
1
2
H
1
6
0
G
2
0
6
W
2
0
7
K
2
1
0
[1]5d9t.a . . . . . . . . . . . *
[1]5d9v.a . . * . . . . * . . . . Ca
[1]5d9w.a . . S . . . . * . . . .
[1]5d9x.a . . S . . . . . . . . . Ca

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
5d9t.a is apo
5d9v.a is apo
5d9w.a:asc
5d9x.a:gsh
[1] 5d9t.a
-
- 0.7 0.8
[1] 5d9v.a -
-
0.4 1.7
[1] 5d9w.a - -
0.1
1.2
[1] 5d9x.a - - 0.3
0.1
[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
5d9t.a
5d9v.a
5d9w.a
5d9x.a
[1] 5d9t.a
0
.08 .04 .09
[1] 5d9v.a .08
0
.04 .16
[1] 5d9w.a .04 .04
0
.12
[1] 5d9x.a .09 .16 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
5d9t.a
5d9v.a
5d9w.a
5d9x.a
[1] 5d9t.a
0
0.2 0.2 0.2
[1] 5d9v.a 0.2
0
0.3 0.2
[1] 5d9w.a 0.2 0.3
0
0.2
[1] 5d9x.a 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
5d9t.a
5d9v.a
5d9w.a
5d9x.a
[1] 5d9t.a
0
0.9 0.3 0.5
[1] 5d9v.a 0.9
0
0.9 0.8
[1] 5d9w.a 0.3 0.9
0
0.6
[1] 5d9x.a 0.5 0.8 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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