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AROE_HELPY_1_263

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROE_HELPY):R: Shikimate binding (16, 18)
8, 63:66, 69, 90, 105, 210, 234, 237
8, 16, 18, 63:66, 69, 90, 105, 210, 234, 237

Full PDB list

3phg, 3phh, 3phi, 3phj, 4foo, 4fos, 4fpx, 4fq8, 4fr5, 4fsh (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
8
S
1
6
S
1
8
N
6
3
V
6
4
T
6
5
K
6
9
N
9
0
D
1
0
5
Y
2
1
0
L
2
3
4
Q
2
3
7
[1]3phg.a none . . . . . . . . . . . .
[1]3phh.a skm12 . . . . . . . . . . . .
[1]3phj.a dhk12 . . . . . . . . . . . .
[1]4foo.a none . . . . . . . . . . . K
[1]4fos.a skm12 . . . . . . . . . . . A
[1]4fpx.a none . . . . . . . . . . . N
[1]4fq8.b skm12 . . . . . . . . . A . .
[1]4fr5.b skm12 . . . . . . . . . S . .

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
V
8
S
1
6
S
1
8
N
6
3
V
6
4
T
6
5
L
6
6
K
6
9
N
9
0
D
1
0
5
Y
2
1
0
L
2
3
4
Q
2
3
7
[1]3phg.a . . . . . . . . . . . . .
[1]3phh.a . . . . . . . . . . . . .
[1]3phj.a . . . . . . . . . . . . .
[1]4foo.a . . . . . . . . . . . . K
[1]4fos.a . . . . . . . . . . . . A
[1]4fpx.a . . . . . . . . . . . . N
[1]4fq8.b . . . . . . . . . . A . .
[1]4fr5.b . . . . . . . . . . S . .

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
3phg.a is apo
3phh.a:skm
3phj.a:dhk
4foo.a is apo
4fos.a:skm
4fpx.a is apo
4fq8.b:skm
4fr5.b:skm
[1] 3phg.a
-
0.2 0.2 - 0.1 - 0.1 0.2
[1] 3phh.a -
0
0 - 0.1 - 0.1 0.1
[1] 3phj.a - 0.1
0
- 0 - 0.1 0
[1] 4foo.a - 1.0 0.7
-
1.0 - 0.8 0.8
[1] 4fos.a - 0.1 0.1 -
0
- 0.2 0.2
[1] 4fpx.a - 0.1 0 - 0.1
-
0.1 0.3
[1] 4fq8.b - 0 0 - 0 -
0
0
[1] 4fr5.b - 0 0 - 0.1 - 0.1
0.2
[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
3phg.a
3phh.a
3phj.a
4foo.a
4fos.a
4fpx.a
4fq8.b
4fr5.b
[1] 3phg.a
0
.01 .02 .08 .01 .04 .02 .02
[1] 3phh.a .01
0
.03 .08 .02 .03 .02 .01
[1] 3phj.a .02 .03
0
.08 .02 .03 .01 .04
[1] 4foo.a .08 .08 .08
0
.08 .10 .08 .08
[1] 4fos.a .01 .02 .02 .08
0
.05 .02 .02
[1] 4fpx.a .04 .03 .03 .10 .05
0
.02 .04
[1] 4fq8.b .02 .02 .01 .08 .02 .02
0
.03
[1] 4fr5.b .02 .01 .04 .08 .02 .04 .03
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
3phg.a
3phh.a
3phj.a
4foo.a
4fos.a
4fpx.a
4fq8.b
4fr5.b
[1] 3phg.a
0
0.3 0.3 0.2 0.3 0.3 0.6 0.5
[1] 3phh.a 0.3
0
0.2 0.3 0.1 0.3 0.6 0.6
[1] 3phj.a 0.3 0.2
0
0.3 0.2 0.3 0.6 0.6
[1] 4foo.a 0.2 0.3 0.3
0
0.3 0.2 0.6 0.6
[1] 4fos.a 0.3 0.1 0.2 0.3
0
0.3 0.6 0.6
[1] 4fpx.a 0.3 0.3 0.3 0.2 0.3
0
0.7 0.6
[1] 4fq8.b 0.6 0.6 0.6 0.6 0.6 0.7
0
0.2
[1] 4fr5.b 0.5 0.6 0.6 0.6 0.6 0.6 0.2
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

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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
3phg.a
3phh.a
3phj.a
4foo.a
4fos.a
4fpx.a
4fq8.b
4fr5.b
[1] 3phg.a
0
0.3 0.4 0.5 0.4 0.5 0.7 0.7
[1] 3phh.a 0.3
0
0.2 0.5 0.2 0.5 0.7 0.7
[1] 3phj.a 0.4 0.2
0
0.6 0.2 0.5 0.7 0.7
[1] 4foo.a 0.5 0.5 0.6
0
0.5 0.5 0.8 0.7
[1] 4fos.a 0.4 0.2 0.2 0.5
0
0.4 0.7 0.7
[1] 4fpx.a 0.5 0.5 0.5 0.5 0.4
0
0.9 0.8
[1] 4fq8.b 0.7 0.7 0.7 0.8 0.7 0.9
0
0.6
[1] 4fr5.b 0.7 0.7 0.7 0.7 0.7 0.8 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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