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CSK21_HUMAN_1_335_beta

Casein kinase II subunit alpha [Protein kinase superfamily. Ser/Thr protein kinase family. CK2 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CSK21_HUMAN):R: Interaction with beta subunit (36, 37, 39:41)
D: Protein kinase (39:41, 52, 59, 67, 69, 101:106, 108:110)
36, 37, 39:41, 52, 59, 67, 69, 101:106, 108:110

Full PDB list

1jwh, 1na7, 1pjk, 2pvr, 2r7i, 2zjw, 3amy, 3at2, 3at3, 3at4, 3axw, 3bqc, 3c13, 3h30, 3mb6, 3mb7, 3nga, 3owj, 3owk, 3owl, 3pe1, 3pe2, 3q9w, 3q9x, 3q9y, 3q9z, 3r0t, 3rps, 3u4u, 3u9c, 3wik, 3wil, 4fbx, 4grb, 4gub, 4kwp, 4nh1, 4rll, 4ub7, 4uba, 5b0x, 5clp, 5cqu, 5cqw, 5cs6, 5csh, 5csp, 5ct0, 5ctp, 5cu0, 5cu2, 5cu3, 5cu4, 5cvf, 5cvh, 5cx9, 5h8b, 5h8e, 5h8g, 5kwh, 5m44, 5m4c, 5m4f, 5m4i, 5mmf, 5mmr, 5mo5, 5mo6, 5mo7, 5mo8, 5mod, 5moe, 5moh, 5mot, 5mov, 5mow, 5mp8, 5mpj, 5n1v, 5nqc (redundant Pocketome entry); 3fwq, 3juh, 3nsz, 3q04, 3qa0, 3u87, 3w8l, 3war, 3wow, 4dgl, 4ib5, 4md7, 4md8, 4md9, 5csv, 5cu6, 5cvg (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
3
6
D
3
7
Y
3
9
Q
4
0
L
4
1
I
5
9
V
6
7
I
6
9
V
1
0
1
K
1
0
2
D
1
0
3
P
1
0
4
T
1
0
8
A
1
1
0
[1]1jwh.a LYGFK44 . . . . . . . . . . . . . .
[1]3h30.a rfz20 . . . . . . . . . . . . . .
[1]4nh1.a YGFK36 . . . . . . . . . . . . . .
[1]5clp.a 42j11 . . . . . . . . . . . . . .
[1]5csh.a 54e15 . . . . . . . . . . . . . .
[1]5cu0.a 54r16 . . . . . . . . . . . . . .
[1]5cu2.a 55118 . . . . . . . . . . . . . .
[1]5mmr.a h8320 . . . . . . . . . . . . . .
[1]5moe.a oqc14 . . . . . . . . . . . . . .
[1]5mp8.a none . . . . . . . . . . . . . .
[1]5nqc.a 1kp10 . . . . . . . . . . . . . .

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
Q
3
6
D
3
7
Y
3
9
Q
4
0
L
4
1
E
5
2
I
5
9
V
6
7
I
6
9
V
1
0
1
K
1
0
2
D
1
0
3
P
1
0
4
V
1
0
5
S
1
0
6
T
1
0
8
P
1
0
9
A
1
1
0
[1]1jwh.a . . . . . . . . . . . . . . . . . .
[1]3h30.a . . . . . . . . . . . * * . . . . .
[1]4nh1.a . * . . . . . . . . . . . . . . . .
[1]5clp.a * . . * . . . . . . . . . . . . . .
[1]5csh.a . . . . . . . . . . . . . . . . . .
[1]5cu0.a . . . . . . . . . . . * . . . . . .
[1]5cu2.a . . . . . . . . . . . * . . . . . .
[1]5mmr.a . . . . . . . . . . . . . . . . . .
[1]5moe.a * . . . . . . . . . . * . . . . . .
[1]5mp8.a * . . . . . . . . . . * . . . . . .
[1]5nqc.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
1jwh.a:LYGFK
3h30.a:rfz
4nh1.a:YGFK
5clp.a:42j
5csh.a:54e
5cu0.a:54r
5cu2.a:551
5mmr.a:h83
5moe.a:oqc
5mp8.a is apo
5nqc.a:1kp
[1] 1jwh.a
0.5
0.3 0.1 0.1 0.6 0.8 0.6 1.1 0.4 - 0.3
[1] 3h30.a 4.0
0.1
3.0 0.6 2.5 2.3 2.6 2.9 2.0 - 0.2
[1] 4nh1.a 1.2 0.1
0
0.2 0.5 0.5 0.6 0.6 0.3 - 0.4
[1] 5clp.a 2.4 1.1 1.2
0
1.0 1.2 1.3 1.4 0.6 - 0.3
[1] 5csh.a 1.5 0 0.6 0.3
0
0 0 0 0 - 0
[1] 5cu0.a 1.5 0.1 0.6 0.1 0
0
0 0 0.1 - 0
[1] 5cu2.a 1.8 0.2 0.5 0.2 0 0
0
0.1 0 - 0
[1] 5mmr.a 1.2 0.1 0.3 0.2 0 0 0
0
0 - 0
[1] 5moe.a 1.8 0.1 1.0 0.1 0 0.2 0.2 0.4
0
- 0
[1] 5mp8.a 2.9 2.5 3.8 1.8 2.5 2.3 2.6 2.7 2.6
-
2.5
[1] 5nqc.a 3.1 0.1 2.6 0.4 2.4 2.3 2.6 2.6 1.9 -
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
1jwh.a
3h30.a
4nh1.a
5clp.a
5csh.a
5cu0.a
5cu2.a
5mmr.a
5moe.a
5mp8.a
5nqc.a
[1] 1jwh.a
0
.31 .10 .11 .13 .12 .13 .11 .08 .20 .26
[1] 3h30.a .31
0
.29 .34 .21 .20 .20 .22 .25 .32 .11
[1] 4nh1.a .10 .29
0
.17 .13 .11 .13 .10 .11 .25 .25
[1] 5clp.a .11 .34 .17
0
.17 .16 .17 .15 .14 .20 .30
[1] 5csh.a .13 .21 .13 .17
0
.02 .02 .02 .06 .23 .17
[1] 5cu0.a .12 .20 .11 .16 .02
0
.03 .02 .05 .22 .16
[1] 5cu2.a .13 .20 .13 .17 .02 .03
0
.04 .06 .21 .15
[1] 5mmr.a .11 .22 .10 .15 .02 .02 .04
0
.05 .24 .18
[1] 5moe.a .08 .25 .11 .14 .06 .05 .06 .05
0
.19 .20
[1] 5mp8.a .20 .32 .25 .20 .23 .22 .21 .24 .19
0
.28
[1] 5nqc.a .26 .11 .25 .30 .17 .16 .15 .18 .20 .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1jwh.a
3h30.a
4nh1.a
5clp.a
5csh.a
5cu0.a
5cu2.a
5mmr.a
5moe.a
5mp8.a
5nqc.a
[1] 1jwh.a
0
1.8 0.7 0.5 0.9 0.9 0.9 0.9 0.8 1.1 1.8
[1] 3h30.a 1.8
0
1.8 1.7 1.5 1.5 1.5 1.5 1.5 1.6 0.4
[1] 4nh1.a 0.7 1.8
0
0.6 0.8 0.8 0.7 0.7 0.7 1.3 1.8
[1] 5clp.a 0.5 1.7 0.6
0
0.7 0.8 0.7 0.7 0.7 1.0 1.7
[1] 5csh.a 0.9 1.5 0.8 0.7
0
0.2 0.2 0.2 0.3 1.1 1.4
[1] 5cu0.a 0.9 1.5 0.8 0.8 0.2
0
0.1 0.1 0.4 1.1 1.4
[1] 5cu2.a 0.9 1.5 0.7 0.7 0.2 0.1
0
0.1 0.4 1.1 1.4
[1] 5mmr.a 0.9 1.5 0.7 0.7 0.2 0.1 0.1
0
0.3 1.1 1.4
[1] 5moe.a 0.8 1.5 0.7 0.7 0.3 0.4 0.4 0.3
0
1.1 1.5
[1] 5mp8.a 1.1 1.6 1.3 1.0 1.1 1.1 1.1 1.1 1.1
0
1.6
[1] 5nqc.a 1.8 0.4 1.8 1.7 1.4 1.4 1.4 1.4 1.5 1.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
1jwh.a
3h30.a
4nh1.a
5clp.a
5csh.a
5cu0.a
5cu2.a
5mmr.a
5moe.a
5mp8.a
5nqc.a
[1] 1jwh.a
0
2.2 1.3 1.5 1.5 1.5 1.6 1.4 1.2 1.6 2.1
[1] 3h30.a 2.2
0
2.2 2.2 1.9 1.9 2.0 1.9 1.9 2.2 0.9
[1] 4nh1.a 1.3 2.2
0
1.2 1.3 1.3 1.2 1.2 1.2 1.7 2.2
[1] 5clp.a 1.5 2.2 1.2
0
1.5 1.4 1.1 1.3 1.4 1.4 2.2
[1] 5csh.a 1.5 1.9 1.3 1.5
0
0.5 0.9 0.6 0.8 1.6 1.9
[1] 5cu0.a 1.5 1.9 1.3 1.4 0.5
0
0.8 0.3 0.9 1.6 1.9
[1] 5cu2.a 1.6 2.0 1.2 1.1 0.9 0.8
0
0.8 1.1 1.6 2.0
[1] 5mmr.a 1.4 1.9 1.2 1.3 0.6 0.3 0.8
0
0.9 1.6 1.9
[1] 5moe.a 1.2 1.9 1.2 1.4 0.8 0.9 1.1 0.9
0
1.4 1.8
[1] 5mp8.a 1.6 2.2 1.7 1.4 1.6 1.6 1.6 1.6 1.4
0
2.1
[1] 5nqc.a 2.1 0.9 2.2 2.2 1.9 1.9 2.0 1.9 1.8 2.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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