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MHCKA_DICDI_551_809

Myosin heavy chain kinase A [Protein kinase superfamily. Alpha-type protein kinase family. ALPK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (MHCKA_DICDI):R: Catalytic (586:592, 594, 643, 645, 647, 689, 713:716, 720, 722, 756, 758, 765, 766)
D: Alpha-type protein kinase (586:592, 594, 643, 645, 647, 689, 713:716, 720, 722, 756, 758, 765, 766)
586:592, 594, 643, 645, 647, 689, 713:716, 720, 722, 756, 758, 765, 766

Full PDB list

3lkm, 3lla, 3lmh, 3lmi, 3pdt, 4zme, 4zmf, 4zs4, 5dyj, 5e4h, 5e9e

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
5
8
6
A
5
8
7
E
5
8
8
G
5
8
9
A
5
9
0
L
5
9
1
R
5
9
2
V
6
4
3
K
6
4
5
L
6
8
9
E
7
1
3
P
7
1
4
L
7
1
5
L
7
1
6
F
7
2
0
K
7
2
2
Q
7
5
8
T
7
6
5
D
7
6
6
[1]3lkm.a amp,mg24 . . . . . . . . . . . . . . . . . . .
[1]3lla.a acp31 . . . . . . . . . . . . . . . . . . .
[1]3lmh.a adp27 . . . . . . . . . . . . . . . . . . *
[1]3lmi.a atp,mg32 . . . . . . . . . . . . . . . . . . A
[1]3pdt.a adp27 . . . . . . . . . . . . . . . . . . .
[1]4zme.a adn19 . . . . . . . . . . . . . . . . . . *
[1]4zmf.b amp23 . . . . . . . . . . . . . . . . . . *
[1]4zs4.a atp31 . . . . . . . . . . . . . . . . . . .
[1]5dyj.a amp23 . . . . . . . . . . . . . . . . . . .
[1]5e4h.c none . . . - - . . . . . . . . . . . . . .
[1]5e9e.b anp31 . . . . . . . . . . . . . . . . . . .

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
5
8
6
A
5
8
7
E
5
8
8
G
5
8
9
A
5
9
0
L
5
9
1
R
5
9
2
A
5
9
4
V
6
4
3
K
6
4
5
Y
6
4
7
L
6
8
9
E
7
1
3
P
7
1
4
L
7
1
5
L
7
1
6
F
7
2
0
K
7
2
2
D
7
5
6
Q
7
5
8
T
7
6
5
D
7
6
6
[1]3lkm.a . . . . . . . . . . . . . . . . . . . . . .
[1]3lla.a . . . . . . . . . . . . . . . . . . . . . .
[1]3lmh.a . . . . . . . . . . . . . . . . . . . . . *
[1]3lmi.a . . . . . . . . . . . . . . . . . . . . . A
[1]3pdt.a . . . . . . . . . . . . . . . . . . . . . .
[1]4zme.a . . . . . . . . . . . . . . . . . . . . . *
[1]4zmf.b . . . . . . . . . . . . . . . . . . . . . *
[1]4zs4.a . . . . . . . . . . . . . . . . . . A . . .
[1]5dyj.a . . . . . . . . . . . . . . . . . . . . . .
[1]5e4h.c . . . - - . * . . . . . . . . . . . . . . *
[1]5e9e.b . . . . . . . . . . . . . . . . . . . . . .

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
3lkm.a:amp,mg
3lla.a:acp
3lmh.a:adp
3lmi.a:atp,mg
3pdt.a:adp
4zme.a:adn
4zmf.b:amp
4zs4.a:atp
5dyj.a:amp
5e4h.c is apo
5e9e.b:anp
[1] 3lkm.a
0
1.2 0.5 0.9 0.1 0.3 0.2 0.4 0.1 - 0.2
[1] 3lla.a 0.1
0
0.1 0.1 0.1 0.1 0 0.1 0 - 0.2
[1] 3lmh.a 0.1 0.3
0.1
0.1 0 0 0 0.2 0 - 0
[1] 3lmi.a 0.3 0.3 0.5
0
0 0 0 0.2 0 - 0.7
[1] 3pdt.a 0 0.6 0.4 0.3
0
0.2 0 0.1 0 - 0.1
[1] 4zme.a 0.1 0 0.1 0.1 0.1
0
0 0.1 0 - 0.1
[1] 4zmf.b 0.1 0.1 0.1 0.1 0.1 0
0
0.1 0 - 0
[1] 4zs4.a 0.2 0.5 0.4 0.1 0.2 0 0
0
0 - 0.3
[1] 5dyj.a 0.7 0.3 0.1 0.1 0.3 0 0 0.4
0
- 0.2
[1] 5e4h.c 2.9 2.3 2.4 1.7 2.0 0.3 2.5 2.2 1.8
-
2.8
[1] 5e9e.b 0.1 0.5 0.2 0.4 0.1 0.3 0 0.2 0 -
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
3lkm.a
3lla.a
3lmh.a
3lmi.a
3pdt.a
4zme.a
4zmf.b
4zs4.a
5dyj.a
5e4h.c
5e9e.b
[1] 3lkm.a
0
.07 .06 .10 .03 .08 .08 .07 .09 .19 .05
[1] 3lla.a .07
0
.03 .03 .05 .01 .01 .04 .03 .14 .03
[1] 3lmh.a .06 .03
0
.05 .03 .01 .01 .04 .03 .16 .02
[1] 3lmi.a .10 .03 .05
0
.06 .04 .04 .04 .05 .16 .06
[1] 3pdt.a .03 .05 .03 .06
0
.05 .05 .04 .05 .17 .03
[1] 4zme.a .08 .01 .01 .04 .05
0
0 .04 .04 .15 .04
[1] 4zmf.b .08 .01 .01 .04 .05 0
0
.04 .04 .15 .04
[1] 4zs4.a .07 .04 .04 .04 .04 .04 .04
0
.03 .15 .04
[1] 5dyj.a .09 .03 .03 .05 .05 .04 .04 .03
0
.14 .05
[1] 5e4h.c .19 .14 .16 .16 .17 .15 .15 .15 .14
0
.17
[1] 5e9e.b .05 .03 .02 .06 .03 .04 .04 .04 .05 .17
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
3lkm.a
3lla.a
3lmh.a
3lmi.a
3pdt.a
4zme.a
4zmf.b
4zs4.a
5dyj.a
5e4h.c
5e9e.b
[1] 3lkm.a
0
1.0 0.9 0.9 0.5 1.0 1.1 0.6 0.9 1.8 0.6
[1] 3lla.a 1.0
0
0.3 0.5 0.6 0.3 0.2 0.4 0.3 1.2 0.5
[1] 3lmh.a 0.9 0.3
0
0.5 0.5 0.2 0.3 0.4 0.2 1.3 0.4
[1] 3lmi.a 0.9 0.5 0.5
0
0.5 0.6 0.6 0.4 0.5 1.4 0.5
[1] 3pdt.a 0.5 0.6 0.5 0.5
0
0.6 0.7 0.3 0.5 1.5 0.3
[1] 4zme.a 1.0 0.3 0.2 0.6 0.6
0
0.3 0.5 0.3 1.2 0.5
[1] 4zmf.b 1.1 0.2 0.3 0.6 0.7 0.3
0
0.6 0.4 1.1 0.6
[1] 4zs4.a 0.6 0.4 0.4 0.4 0.3 0.5 0.6
0
0.4 1.4 0.2
[1] 5dyj.a 0.9 0.3 0.2 0.5 0.5 0.3 0.4 0.4
0
1.3 0.3
[1] 5e4h.c 1.8 1.2 1.3 1.4 1.5 1.2 1.1 1.4 1.3
0
1.5
[1] 5e9e.b 0.6 0.5 0.4 0.5 0.3 0.5 0.6 0.2 0.3 1.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
3lkm.a
3lla.a
3lmh.a
3lmi.a
3pdt.a
4zme.a
4zmf.b
4zs4.a
5dyj.a
5e4h.c
5e9e.b
[1] 3lkm.a
0
1.1 1.0 1.0 0.7 1.2 1.2 0.9 1.1 2.2 0.9
[1] 3lla.a 1.1
0
0.6 0.6 0.9 0.8 0.8 0.9 0.7 1.7 0.8
[1] 3lmh.a 1.0 0.6
0
0.8 0.9 0.7 0.8 0.8 0.8 1.9 0.7
[1] 3lmi.a 1.0 0.6 0.8
0
0.8 1.0 1.0 0.9 0.8 1.8 0.9
[1] 3pdt.a 0.7 0.9 0.9 0.8
0
1.1 1.1 0.9 1.0 2.0 0.9
[1] 4zme.a 1.2 0.8 0.7 1.0 1.1
0
0.3 0.7 0.7 1.8 0.5
[1] 4zmf.b 1.2 0.8 0.8 1.0 1.1 0.3
0
0.7 0.7 1.7 0.6
[1] 4zs4.a 0.9 0.9 0.8 0.9 0.9 0.7 0.7
0
0.8 1.9 0.5
[1] 5dyj.a 1.1 0.7 0.8 0.8 1.0 0.7 0.7 0.8
0
1.8 0.7
[1] 5e4h.c 2.2 1.7 1.9 1.8 2.0 1.8 1.7 1.9 1.8
0
2.0
[1] 5e9e.b 0.9 0.8 0.7 0.9 0.9 0.5 0.6 0.5 0.7 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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