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AROE_VIBCH_1_278

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROE_VIBCH):R: Shikimate binding (18, 20)
10, 63:65, 69, 90, 106, 245, 248
10, 18, 20, 63:65, 69, 90, 106, 245, 248

Full PDB list

3o8q, 3pgj, 3sef (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
1
0
S
1
8
S
2
0
N
6
3
T
6
5
K
6
9
N
9
0
D
1
0
6
L
2
4
5
Q
2
4
8
[1]3o8q.a none . . . . . . . . . .
[1]3pgj.c 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
1
0
S
1
8
S
2
0
N
6
3
V
6
4
T
6
5
K
6
9
N
9
0
D
1
0
6
L
2
4
5
Q
2
4
8
[1]3o8q.a . . . . . . . . . . .
[1]3pgj.c . . . . . . . . . . .

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
3o8q.a is apo
3pgj.c:skm
[1] 3o8q.a
-
0
[1] 3pgj.c -
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
3o8q.a
3pgj.c
[1] 3o8q.a
0
.01
[1] 3pgj.c .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3o8q.a
3pgj.c
[1] 3o8q.a
0
0.7
[1] 3pgj.c 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 Å)

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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
3o8q.a
3pgj.c
[1] 3o8q.a
0
0.9
[1] 3pgj.c 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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