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KS6A3_HUMAN_398_740

Ribosomal protein S6 kinase alpha-3 [Protein kinase superfamily. AGC Ser/Thr protein kinase family. S6 kinase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (KS6A3_HUMAN):D: Protein kinase 2 (428:436, 449, 451, 467, 477, 491, 493:497, 499, 500, 543, 544, 546, 560, 561)428:436, 449, 451, 467, 477, 491, 493:497, 499, 500, 543, 544, 546, 560, 561
Metals (Me):Na

Full PDB list

2qr7, 2qr8, 4d9t, 4d9u, 4jg6, 4jg7, 4jg8, 4m8t, 4mao

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
4
2
8
G
4
2
9
V
4
3
0
G
4
3
1
S
4
3
4
V
4
3
5
C
4
3
6
A
4
4
9
K
4
5
1
L
4
6
7
I
4
7
7
V
4
9
1
T
4
9
3
E
4
9
4
L
4
9
5
M
4
9
6
G
4
9
9
S
5
4
3
N
5
4
4
L
5
4
6
C
5
6
0
D
5
6
1
[1]2qr7.a none . . . . . . . . . . . . . . . * . . . . . . Na
[1]2qr8.a none . . . . . . . . . . . . . . . . . . . . . . Na
[1]4d9t.a 0jg29 . . . . . . . . . . . . . . . . . . . . . . Na
[1]4d9u.a 0jh32 . . . . . . * . . . . . . . . . . . . . . . Na
[1]4jg6.a 1lb16 . - - - . . * . . . . . . . . . . . . . . . Na
[1]4jg7.a 1lc24 . . . - . . * . . . . . . . . . . . . . . . Na
[1]4jg8.a 1le33 . . . . . . * . . . . . M . . . . . . . . .
[1]4m8t.a rmm18 . . . . . . * . . . . . M . . . . . . . . . Na
[1]4mao.a 28d30 . . . . . . * . . . . . M . . . . . . . . . Na

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
I
4
2
8
G
4
2
9
V
4
3
0
G
4
3
1
S
4
3
2
Y
4
3
3
S
4
3
4
V
4
3
5
C
4
3
6
A
4
4
9
K
4
5
1
L
4
6
7
I
4
7
7
V
4
9
1
T
4
9
3
E
4
9
4
L
4
9
5
M
4
9
6
K
4
9
7
G
4
9
9
E
5
0
0
S
5
4
3
N
5
4
4
L
5
4
6
C
5
6
0
D
5
6
1
[1]2qr7.a . . . . . . . . . . . . . . . . . * . . . . . . . . Na
[1]2qr8.a . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]4d9t.a . . . . . . . . * . . . . . . . . . . . . . . . . . Na
[1]4d9u.a . . . . . . . . * . . . . . . . . . . . . . . . . . Na
[1]4jg6.a . - - - - - . . * . . . . . . . . . . . . . . . . . Na
[1]4jg7.a . * . - - . * . * . . . . . . . . . . . . . . . . . Na
[1]4jg8.a . . . . . . . . * . . . . . M . . . . . . . . . . .
[1]4m8t.a . . * . . . . . * . . . . . M . . . . . . . . . . . Na
[1]4mao.a . . * . . . . . * . . . . . M . . . . . . . . . . . Na

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
2qr7.a is apo
2qr8.a is apo
4d9t.a:0jg
4d9u.a:0jh
4jg6.a:1lb
4jg7.a:1lc
4jg8.a:1le
4m8t.a:rmm
4mao.a:28d
[1] 2qr7.a
-
- 0.4 0.5 0.3 0.3 0.4 0.4 0.3
[1] 2qr8.a -
-
0.3 0.6 0.2 0.4 0.4 0.3 0.3
[1] 4d9t.a - -
0.3
0.5 0.4 0.7 0.7 0.6 0.3
[1] 4d9u.a - - 0.3
0.3
0.4 0.8 0.7 0.6 0.6
[1] 4jg6.a - - 0.5 1.1
0.4
0.9 1.0 0.6 0.4
[1] 4jg7.a - - 2.7 4.9 0.5
0.6
2.9 1.9 0.6
[1] 4jg8.a - - 1.9 2.0 0.5 0.5
0.5
0.6 0.4
[1] 4m8t.a - - 1.6 2.4 0.4 0.7 0.6
0.6
0.4
[1] 4mao.a - - 2.2 3.8 0.6 0.9 1.7 1.4
0.4
[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
2qr7.a
2qr8.a
4d9t.a
4d9u.a
4jg6.a
4jg7.a
4jg8.a
4m8t.a
4mao.a
[1] 2qr7.a
0
.02 .04 .05 .06 .20 .08 .12 .17
[1] 2qr8.a .02
0
.04 .03 .04 .19 .07 .10 .16
[1] 4d9t.a .04 .04
0
.01 .03 .18 .08 .09 .16
[1] 4d9u.a .05 .03 .01
0
.02 .18 .08 .08 .15
[1] 4jg6.a .06 .04 .03 .02
0
.17 .09 .08 .15
[1] 4jg7.a .20 .19 .18 .18 .17
0
.23 .24 .30
[1] 4jg8.a .08 .07 .08 .08 .09 .23
0
.07 .12
[1] 4m8t.a .12 .10 .09 .08 .08 .24 .07
0
.07
[1] 4mao.a .17 .16 .16 .15 .15 .30 .12 .07
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
2qr7.a
2qr8.a
4d9t.a
4d9u.a
4jg6.a
4jg7.a
4jg8.a
4m8t.a
4mao.a
[1] 2qr7.a
0
0.3 0.6 0.7 0.5 2.1 0.6 1.0 1.5
[1] 2qr8.a 0.3
0
0.6 0.6 0.4 2.1 0.6 1.1 1.6
[1] 4d9t.a 0.6 0.6
0
0.3 0.6 2.1 0.7 1.1 1.4
[1] 4d9u.a 0.7 0.6 0.3
0
0.6 2.0 0.7 1.0 1.3
[1] 4jg6.a 0.5 0.4 0.6 0.6
0
0.8 0.4 0.4 0.7
[1] 4jg7.a 2.1 2.1 2.1 2.0 0.8
0
2.0 1.8 1.9
[1] 4jg8.a 0.6 0.6 0.7 0.7 0.4 2.0
0
0.9 1.4
[1] 4m8t.a 1.0 1.1 1.1 1.0 0.4 1.8 0.9
0
1.0
[1] 4mao.a 1.5 1.6 1.4 1.3 0.7 1.9 1.4 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
2qr7.a
2qr8.a
4d9t.a
4d9u.a
4jg6.a
4jg7.a
4jg8.a
4m8t.a
4mao.a
[1] 2qr7.a
0
0.5 0.8 0.9 0.8 1.9 0.7 1.2 1.6
[1] 2qr8.a 0.5
0
0.8 1.0 0.8 1.8 0.7 1.3 1.7
[1] 4d9t.a 0.8 0.8
0
0.8 0.7 1.9 0.9 1.1 1.5
[1] 4d9u.a 0.9 1.0 0.8
0
0.8 1.9 1.0 1.2 1.4
[1] 4jg6.a 0.8 0.8 0.7 0.8
0
0.9 0.8 0.5 0.8
[1] 4jg7.a 1.9 1.8 1.9 1.9 0.9
0
1.8 1.7 1.8
[1] 4jg8.a 0.7 0.7 0.9 1.0 0.8 1.8
0
1.2 1.5
[1] 4m8t.a 1.2 1.3 1.1 1.2 0.5 1.7 1.2
0
1.0
[1] 4mao.a 1.6 1.7 1.5 1.4 0.8 1.8 1.5 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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