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AROK_MYCTU_1_176

Shikimate kinase [Shikimate kinase family]

Composition of the binding site

Protein chains monomer
A1 (AROK_MYCTU):10:18, 34, 45, 49, 57, 58, 61, 79:81, 106, 109:111, 132, 136, 150:155, 15810:18, 34, 45, 49, 57, 58, 61, 79:81, 106, 109:111, 116:119, 132, 136, 150:155, 158

Full PDB list

1l4u, 1l4y, 1u8a, 1we2, 1zyu, 2dfn, 2dft, 2g1j, 2g1k, 2iyq, 2iyr, 2iys, 2iyt, 2iyu, 2iyv, 2iyw, 2iyx, 2iyy, 2iyz, 3baf, 4bqs (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
P
1
1
G
1
2
S
1
3
G
1
4
K
1
5
S
1
6
T
1
7
D
3
4
I
4
5
F
4
9
F
5
7
R
5
8
G
7
9
G
8
0
G
8
1
R
1
1
0
R
1
1
7
P
1
1
8
L
1
1
9
R
1
3
6
T
1
5
0
R
1
5
3
N
1
5
4
P
1
5
5
V
1
5
8
[1]1we2.a adp,dhk,mg40 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zyu.a acp,skm43 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dft.b adp,mg28 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2g1j.b none . . . . . . . . . . . . . . . . - - - . . . . . .
[1]2iyq.a adp,skm39 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyv.a adp27 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyw.a atp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyx.a skm12 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyy.a s3p16 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyz.a adp,s3p43 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3baf.a anp,skm43 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bqs.a adp,k2q42 . . . . . . . . . . . . . . . . . . . . . . . . .

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
L
1
0
P
1
1
G
1
2
S
1
3
G
1
4
K
1
5
S
1
6
T
1
7
I
1
8
D
3
4
I
4
5
F
4
9
F
5
7
R
5
8
E
6
1
G
7
9
G
8
0
G
8
1
E
1
0
6
R
1
0
9
R
1
1
0
T
1
1
1
V
1
1
6
R
1
1
7
P
1
1
8
L
1
1
9
L
1
3
2
R
1
3
6
T
1
5
0
N
1
5
1
R
1
5
2
R
1
5
3
N
1
5
4
P
1
5
5
V
1
5
8
[1]1we2.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]1zyu.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2dft.b . . . . . . . . . . . . . . . . . . . . * . . * . . . * . . . * . . .
[1]2g1j.b . . . . . . * . . . . . . . . . . . . . * . - - - - . . . . . . . . .
[1]2iyq.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . * . . .
[1]2iyv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyw.a . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2iyz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . .
[1]3baf.a . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]4bqs.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
1we2.a:adp,dhk,mg
1zyu.a:acp,skm
2dft.b:adp,mg
2g1j.b is apo
2iyq.a:adp,skm
2iyv.a:adp
2iyw.a:atp,mg
2iyx.a:skm
2iyy.a:s3p
2iyz.a:adp,s3p
3baf.a:anp,skm
4bqs.a:adp,k2q
[1] 1we2.a
0.4
0.5 0.2 - 0.5 1.2 2.7 0.3 0.1 1.3 0.4 0.6
[1] 1zyu.a 0.9
0.4
0.7 - 0.7 1.3 1.2 0.3 0.5 1.0 1.2 0.5
[1] 2dft.b 2.7 2.9
0
- 1.3 2.4 3.7 0.9 1.1 2.9 2.2 1.6
[1] 2g1j.b 2.3 1.8 0.9
-
2.0 1.3 1.4 0.4 0.3 2.8 1.9 2.0
[1] 2iyq.a 0.9 0.8 0 -
0
2.1 3.3 0.1 0 1.0 0.6 0.7
[1] 2iyv.a 0.4 0.3 0.6 - 0.8
0
0.4 0.2 0.3 0.9 0.3 0.4
[1] 2iyw.a 0.6 0.4 0.7 - 0.9 0
0.1
0.2 0.3 1.2 0.3 0.4
[1] 2iyx.a 0.5 0 0.5 - 0.5 0.8 0.7
0
0 0.2 0.3 0.2
[1] 2iyy.a 0.5 0.1 0.8 - 0.8 0.6 0.7 0
0
0.2 0.4 0.3
[1] 2iyz.a 0.4 0 0.7 - 0.5 0.8 1.0 0 0
0
0.2 0.1
[1] 3baf.a 0 0.2 0.1 - 0.1 0.6 1.3 0 0 0.6
0
0
[1] 4bqs.a 0.5 0.2 0.3 - 0.5 1.0 1.3 0.1 0.1 0.8 0.5
0
[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
1we2.a
1zyu.a
2dft.b
2g1j.b
2iyq.a
2iyv.a
2iyw.a
2iyx.a
2iyy.a
2iyz.a
3baf.a
4bqs.a
[1] 1we2.a
0
.10 .13 .15 .06 .09 .11 .10 .10 .09 .07 .08
[1] 1zyu.a .10
0
.16 .12 .09 .07 .09 .06 .07 .06 .08 .04
[1] 2dft.b .13 .16
0
.17 .12 .19 .20 .19 .19 .19 .15 .16
[1] 2g1j.b .15 .12 .17
0
.17 .08 .09 .11 .10 .12 .10 .11
[1] 2iyq.a .06 .09 .12 .17
0
.12 .14 .10 .11 .09 .08 .08
[1] 2iyv.a .09 .07 .19 .08 .12
0
.02 .06 .06 .07 .06 .06
[1] 2iyw.a .11 .09 .20 .09 .14 .02
0
.08 .08 .09 .06 .07
[1] 2iyx.a .10 .06 .19 .11 .10 .06 .08
0
.01 .02 .06 .04
[1] 2iyy.a .10 .07 .19 .10 .11 .06 .08 .01
0
.03 .07 .05
[1] 2iyz.a .09 .06 .19 .12 .09 .07 .09 .02 .03
0
.07 .05
[1] 3baf.a .07 .08 .15 .10 .08 .06 .06 .06 .07 .07
0
.05
[1] 4bqs.a .08 .04 .16 .11 .08 .06 .07 .04 .05 .05 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
1we2.a
1zyu.a
2dft.b
2g1j.b
2iyq.a
2iyv.a
2iyw.a
2iyx.a
2iyy.a
2iyz.a
3baf.a
4bqs.a
[1] 1we2.a
0
1.0 1.2 1.9 0.8 6.3 6.3 0.9 0.9 0.9 1.1 0.9
[1] 1zyu.a 1.0
0
1.3 2.1 0.8 6.4 6.4 0.6 0.6 0.6 1.0 0.6
[1] 2dft.b 1.2 1.3
0
2.7 0.9 6.7 6.7 1.4 1.4 1.4 1.5 1.2
[1] 2g1j.b 1.9 2.1 2.7
0
2.3 1.2 1.3 2.0 2.0 2.0 2.0 2.1
[1] 2iyq.a 0.8 0.8 0.9 2.3
0
6.5 6.5 0.8 0.8 0.8 1.1 0.8
[1] 2iyv.a 6.3 6.4 6.7 1.2 6.5
0
0.5 6.4 6.4 6.4 6.1 6.4
[1] 2iyw.a 6.3 6.4 6.7 1.3 6.5 0.5
0
6.4 6.3 6.4 6.1 6.4
[1] 2iyx.a 0.9 0.6 1.4 2.0 0.8 6.4 6.4
0
0.1 0.4 0.9 0.4
[1] 2iyy.a 0.9 0.6 1.4 2.0 0.8 6.4 6.3 0.1
0
0.4 0.9 0.4
[1] 2iyz.a 0.9 0.6 1.4 2.0 0.8 6.4 6.4 0.4 0.4
0
0.9 0.5
[1] 3baf.a 1.1 1.0 1.5 2.0 1.1 6.1 6.1 0.9 0.9 0.9
0
1.0
[1] 4bqs.a 0.9 0.6 1.2 2.1 0.8 6.4 6.4 0.4 0.4 0.5 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
1we2.a
1zyu.a
2dft.b
2g1j.b
2iyq.a
2iyv.a
2iyw.a
2iyx.a
2iyy.a
2iyz.a
3baf.a
4bqs.a
[1] 1we2.a
0
1.4 1.5 2.2 0.9 6.9 6.9 1.6 1.6 1.3 1.2 1.7
[1] 1zyu.a 1.4
0
1.6 2.3 1.3 6.9 6.8 1.1 1.2 0.7 1.4 1.2
[1] 2dft.b 1.5 1.6
0
3.0 1.3 7.3 7.2 1.8 1.8 1.6 1.7 1.8
[1] 2g1j.b 2.2 2.3 3.0
0
2.5 1.5 1.6 2.2 2.3 2.1 2.4 2.3
[1] 2iyq.a 0.9 1.3 1.3 2.5
0
7.1 7.0 1.5 1.5 1.2 1.2 1.6
[1] 2iyv.a 6.9 6.9 7.3 1.5 7.1
0
0.7 6.9 6.8 6.9 6.8 6.8
[1] 2iyw.a 6.9 6.8 7.2 1.6 7.0 0.7
0
6.8 6.8 6.8 6.7 6.7
[1] 2iyx.a 1.6 1.1 1.8 2.2 1.5 6.9 6.8
0
0.2 1.0 1.5 1.3
[1] 2iyy.a 1.6 1.2 1.8 2.3 1.5 6.8 6.8 0.2
0
0.9 1.5 1.6
[1] 2iyz.a 1.3 0.7 1.6 2.1 1.2 6.9 6.8 1.0 0.9
0
1.3 0.9
[1] 3baf.a 1.2 1.4 1.7 2.4 1.2 6.8 6.7 1.5 1.5 1.3
0
1.8
[1] 4bqs.a 1.7 1.2 1.8 2.3 1.6 6.8 6.7 1.3 1.6 0.9 1.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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