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AROE_STAEQ_1_269

Shikimate dehydrogenase (NADP(+)) [Shikimate dehydrogenase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROE_STAEQ):R: Shikimate binding (13, 15)
5, 58, 60, 64, 85, 100, 236, 239
5, 13, 15, 58, 60, 64, 85, 100, 236, 239

Full PDB list

3don, 3doo

Pocket contact map

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PDB.ch
   
ligand
A1
S
1
3
S
1
5
N
5
8
T
6
0
K
6
4
N
8
5
D
1
0
0
F
2
3
6
Q
2
3
9
[1]3don.a none . . . . . . . . .
[1]3doo.a skm12 . . . . . . . . .

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

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PDB.ch
A1
V
5
S
1
3
S
1
5
N
5
8
T
6
0
K
6
4
N
8
5
D
1
0
0
F
2
3
6
Q
2
3
9
[1]3don.a . . . . . . . . . .
[1]3doo.a . . . . . . . . . .

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
3don.a is apo
3doo.a:skm
[1] 3don.a
-
0.1
[1] 3doo.a -
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
3don.a
3doo.a
[1] 3don.a
0
0
[1] 3doo.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
3don.a
3doo.a
[1] 3don.a
0
0.2
[1] 3doo.a 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
3don.a
3doo.a
[1] 3don.a
0
0.3
[1] 3doo.a 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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