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AROE_AQUAE_1_269

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (AROE_AQUAE):R: Shikimate binding (19, 21)
64, 66, 70, 91, 106, 216, 239, 242
19, 21, 64, 66, 70, 91, 106, 216, 239, 242

Full PDB list

2hk7, 2hk8, 2hk9 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
S
1
9
S
2
1
N
6
4
K
7
0
N
9
1
D
1
0
6
Y
2
1
6
L
2
3
9
Q
2
4
2
[1]2hk8.a none . . . . . . . . .
[1]2hk9.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
S
1
9
S
2
1
N
6
4
T
6
6
K
7
0
N
9
1
D
1
0
6
Y
2
1
6
L
2
3
9
Q
2
4
2
[1]2hk8.a . . . . . . . . . .
[1]2hk9.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
2hk8.a is apo
2hk9.a:skm
[1] 2hk8.a
-
0.2
[1] 2hk9.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
2hk8.a
2hk9.a
[1] 2hk8.a
0
.03
[1] 2hk9.a .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2hk8.a
2hk9.a
[1] 2hk8.a
0
0.5
[1] 2hk9.a 0.5
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
2hk8.a
2hk9.a
[1] 2hk8.a
0
1.6
[1] 2hk9.a 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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