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CDPK4_PLAF7_9_528

Calcium-dependent protein kinase 4 [Protein kinase superfamily. Ser/Thr protein kinase family. CDPK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDPK4_PLAF7):D: Protein kinase (76:79, 84, 97, 99, 131, 133, 145, 147:150, 200, 214, 215, 218)76:79, 84, 97, 99, 131, 133, 145, 147:150, 200, 214, 215, 218

Full PDB list

4qox, 4rgj

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
7
6
G
7
7
K
7
8
G
7
9
V
8
4
A
9
7
K
9
9
M
1
3
1
L
1
3
3
L
1
4
5
S
1
4
7
D
1
4
8
Y
1
5
0
L
2
0
0
I
2
1
4
[1]4qox.a dxr22 . . . . . . . . . . . . . . .
[2]4rgj.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

[download in TSV format]
   
PDB.ch
A1
L
7
6
G
7
7
K
7
8
G
7
9
V
8
4
A
9
7
K
9
9
M
1
3
1
L
1
3
3
L
1
4
5
S
1
4
7
D
1
4
8
V
1
4
9
Y
1
5
0
L
2
0
0
I
2
1
4
D
2
1
5
L
2
1
8
[1]4qox.a . . . . . . . . . . . . . . . . . .
[2]4rgj.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
4qox.a:dxr
4rgj.a is apo
[1] 4qox.a
0
-
[2] 4rgj.a 5.8
-
[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
4qox.a
4rgj.a
[1] 4qox.a
0
.32
[2] 4rgj.a .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
4qox.a
4rgj.a
[1] 4qox.a
0
0.6
[2] 4rgj.a 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
4qox.a
4rgj.a
[1] 4qox.a
0
1.7
[2] 4rgj.a 1.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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