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MP2K4_HUMAN_79_399_ATPsite

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 (108:111, 116, 129, 131, 148, 178:181, 184, 187, 229, 231, 233, 234, 236, 246, 247)108:111, 116, 129, 131, 148, 178:181, 184, 187, 229, 231, 233, 234, 236, 246, 247
Metals (Me):Mg

Full PDB list

3aln, 3alo, 3vut (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
1
0
8
G
1
0
9
R
1
1
0
G
1
1
1
V
1
1
6
A
1
2
9
K
1
3
1
D
1
4
8
M
1
7
8
E
1
7
9
L
1
8
0
M
1
8
1
S
1
8
4
K
1
8
7
D
2
2
9
K
2
3
1
S
2
3
3
N
2
3
4
L
2
3
6
D
2
4
7
[1]3aln.b anp31 . . . . . . . . . . . . . . . . . . . . Mg
[1]3aln.c anp31 - - - - - - - A . . . . . . - . . . . .
[1]3vut.a 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

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PDB.ch
A1 Me
I
1
0
8
G
1
0
9
R
1
1
0
G
1
1
1
V
1
1
6
A
1
2
9
K
1
3
1
D
1
4
8
M
1
7
8
E
1
7
9
L
1
8
0
M
1
8
1
S
1
8
4
K
1
8
7
D
2
2
9
K
2
3
1
S
2
3
3
N
2
3
4
L
2
3
6
C
2
4
6
D
2
4
7
[1]3aln.b . . . . . . . . . . . . . . . . . . . . . Mg
[1]3aln.c - - - - - - - A . . . . . . - . . . . . .
[1]3vut.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
3aln.b:anp
3aln.c:anp
3vut.a is apo
[1] 3aln.b
0.4
1.4 -
[1] 3aln.c 0.2
0
-
[1] 3vut.a 0 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
3aln.b
3aln.c
3vut.a
[1] 3aln.b
0
.07 .07
[1] 3aln.c .07
0
.02
[1] 3vut.a .07 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.3 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.b
3aln.c
3vut.a
[1] 3aln.b
0
5.2 2.1
[1] 3aln.c 5.2
0
5.5
[1] 3vut.a 2.1 5.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.1 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
3aln.b
3aln.c
3vut.a
[1] 3aln.b
0
4.4 3.3
[1] 3aln.c 4.4
0
5.0
[1] 3vut.a 3.3 5.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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