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AROK_HELPY_1_162

Shikimate kinase [Shikimate kinase family]

Composition of the binding site

Protein chains monomer
A1 (AROK_HELPY):9:11, 14, 33, 44, 45, 47:49, 52:54, 56, 57, 79:84, 128, 132, 135, 1369:11, 14, 33, 44, 45, 47:49, 52:54, 56, 57, 79:84, 114:119, 128, 132, 135, 136

Full PDB list

1zuh, 1zui, 3hr7, 3mrs, 3muf, 3n2e (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
9
M
1
0
K
1
4
D
3
3
V
4
4
R
4
5
F
4
8
E
5
3
R
5
7
G
7
9
G
8
0
G
8
1
V
8
3
M
8
4
E
1
1
4
R
1
1
6
P
1
1
7
L
1
1
8
L
1
1
9
R
1
3
2
L
1
3
5
Y
1
3
6
[1]3hr7.a none . . . . . . . . . . . . . . - - - - . . . .
[1]3n2e.b osa33 . . . . . . . . . . . . . . A . . . . . . .
[2]3muf.a s3p16 . . . . . . . . . . . . . . . . . . . . . .
[3]1zui.a skm12 . . . . . . . . . . . . . . . . . . . . . .
[4]3mrs.a none . . . . . . . . A . . . . . - - - - - . . .

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
F
9
M
1
0
G
1
1
K
1
4
D
3
3
V
4
4
R
4
5
I
4
7
F
4
8
E
4
9
G
5
2
E
5
3
D
5
4
F
5
6
R
5
7
G
7
9
G
8
0
G
8
1
I
8
2
V
8
3
M
8
4
E
1
1
4
K
1
1
5
R
1
1
6
P
1
1
7
L
1
1
8
L
1
1
9
L
1
2
8
R
1
3
2
L
1
3
5
Y
1
3
6
[1]3hr7.a . . . . . . . . . . . . . . . . . . . . . - - - - - . . * . .
[1]3n2e.b . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . .
[2]3muf.a . * . . . . . . . . . . . . . . . . . . . . . * * * . . * . .
[3]1zui.a . * . . . . . . . . . . . . . . . . . . . . * * . . . . * . .
[4]3mrs.a . * . . . . . . * . . * . * 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
3hr7.a is apo
3n2e.b:osa
3muf.a:s3p
1zui.a:skm
3mrs.a is apo
[1] 3hr7.a
-
2.0 0.9 0 -
[1] 3n2e.b -
0
0.3 0.1 -
[2] 3muf.a - 12
0.2
0 -
[3] 1zui.a - 13 1.4
0
-
[4] 3mrs.a - 11 6.2 4.9
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
3hr7.a
3n2e.b
3muf.a
1zui.a
3mrs.a
[1] 3hr7.a
0
.09 .32 .38 .55
[1] 3n2e.b .09
0
.39 .46 .51
[2] 3muf.a .32 .39
0
.40 .85
[3] 1zui.a .38 .46 .40
0
.89
[4] 3mrs.a .55 .51 .85 .89
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.5 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
3hr7.a
3n2e.b
3muf.a
1zui.a
3mrs.a
[1] 3hr7.a
0
2.4 3.3 3.3 3.9
[1] 3n2e.b 2.4
0
3.7 4.0 3.3
[2] 3muf.a 3.3 3.7
0
1.7 3.5
[3] 1zui.a 3.3 4.0 1.7
0
3.5
[4] 3mrs.a 3.9 3.3 3.5 3.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.3 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
3hr7.a
3n2e.b
3muf.a
1zui.a
3mrs.a
[1] 3hr7.a
0
2.8 3.4 3.5 4.2
[1] 3n2e.b 2.8
0
4.2 3.9 3.6
[2] 3muf.a 3.4 4.2
0
3.1 3.8
[3] 1zui.a 3.5 3.9 3.1
0
3.8
[4] 3mrs.a 4.2 3.6 3.8 3.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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