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MP2K4_HUMAN_79_399_allosteric

Dual specificity mitogen-activated protein kinase kinase 4 [Protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (MP2K4_HUMAN):D: Protein kinase (121, 126, 128, 144, 146, 165:169, 177)
79:85, 89:98
79:85, 89:98, 121, 126, 128, 144, 146, 165:169, 177
Metals (Me):Mg

Full PDB list

3aln, 3alo, 3vut

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
W
9
5
D
9
6
F
9
7
T
9
8
H
1
2
1
M
1
2
8
Y
1
6
5
A
1
6
7
L
1
6
8
F
1
6
9
C
1
7
7
[1]3aln.a none . . . . . . . . . . . Mg
[1]3alo.a DDEMtpoGYA65 . . . . . . . . . . . Mg
[2]3vut.b none . . . . . . . . . . .

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 Me
H
7
9
S
8
0
I
8
1
E
8
2
S
8
3
S
8
4
G
8
5
I
8
9
S
9
0
P
9
1
E
9
2
Q
9
3
H
9
4
W
9
5
D
9
6
F
9
7
T
9
8
H
1
2
1
Q
1
2
6
M
1
2
8
Q
1
4
4
L
1
4
6
Y
1
6
5
G
1
6
6
A
1
6
7
L
1
6
8
F
1
6
9
C
1
7
7
[1]3aln.a - - - - . . . . . . * . . . . . . . . . . . . . . . . . Mg
[1]3alo.a - - - - - - - - - - - - - . . . . . . . . . . . . . . . Mg
[2]3vut.b M * * * * * * . . * * . . . . . . . . . . . . . . . . .

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
3aln.a is apo
3alo.a:DDEMtpoGYA
3vut.b is apo
[1] 3aln.a
-
4.3 -
[1] 3alo.a -
0
-
[2] 3vut.b - 27
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
3aln.a
3alo.a
3vut.b
[1] 3aln.a
0
.15 .93
[1] 3alo.a .15
0
.94
[2] 3vut.b .93 .94
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.4 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
3aln.a
3alo.a
3vut.b
[1] 3aln.a
0
2.7 9.3
[1] 3alo.a 2.7
0
3.3
[2] 3vut.b 9.3 3.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.7 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
3aln.a
3alo.a
3vut.b
[1] 3aln.a
0
2.4 9.0
[1] 3alo.a 2.4
0
4.1
[2] 3vut.b 9.0 4.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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