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AROE_THET8_1_263

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROE_THET8):R: Shikimate binding (14, 16)
6, 58:60, 64, 85, 100, 207, 232, 235
6, 14, 16, 58:60, 64, 85, 100, 207, 232, 235

Full PDB list

1wxd, 2cy0, 2d5c, 2ev9 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
6
S
1
4
S
1
6
N
5
8
L
5
9
T
6
0
K
6
4
N
8
5
D
1
0
0
Y
2
0
7
Q
2
3
5
[1]2cy0.a none . . . . . . . . . . .
[1]2d5c.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
6
S
1
4
S
1
6
N
5
8
L
5
9
T
6
0
K
6
4
N
8
5
D
1
0
0
Y
2
0
7
L
2
3
2
Q
2
3
5
[1]2cy0.a . . . . . . . . . . . .
[1]2d5c.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
2cy0.a is apo
2d5c.a:skm
[1] 2cy0.a
-
0.1
[1] 2d5c.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
2cy0.a
2d5c.a
[1] 2cy0.a
0
0
[1] 2d5c.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
2cy0.a
2d5c.a
[1] 2cy0.a
0
0.3
[1] 2d5c.a 0.3
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
2cy0.a
2d5c.a
[1] 2cy0.a
0
0.6
[1] 2d5c.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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