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RIO2_ARCFU_1_282

RIO-type serine/threonine-protein kinase Rio2 [Protein kinase superfamily. RIO-type Ser/Thr kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RIO2_ARCFU):D: Protein kinase (98, 103, 104, 106, 118, 120, 122, 126, 167, 179:182, 186, 218, 222, 223, 225, 234, 235, 237)98, 103, 104, 106, 118, 120, 122, 126, 167, 179:182, 186, 218, 222, 223, 225, 234, 235, 237

Full PDB list

1tqi, 1tqm, 1tqp, 1zao, 1zar

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
M
9
8
E
1
0
3
S
1
0
4
V
1
0
6
V
1
1
8
K
1
2
0
H
1
2
2
H
1
2
6
P
1
6
7
M
1
7
9
E
1
8
0
L
1
8
1
I
1
8
2
E
1
8
6
Y
2
2
2
N
2
2
3
L
2
2
5
I
2
3
4
D
2
3
5
P
2
3
7
[1]1tqi.a none . . . . . . . - . . . . . . . . . . . .
[1]1tqm.a anp31 . . . . . . . - . . . . . . . . . . . .
[1]1tqp.a atp31 * . . . . . . - . * . . . . . . . . . .
[1]1zao.a atp,mn,mn33 . . . . . . . . . . . . . . . . . . . .
[1]1zar.a adp,mn28 . . . . . . . - . . . . . . . . . . . .

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
M
9
8
E
1
0
3
S
1
0
4
V
1
0
6
V
1
1
8
K
1
2
0
H
1
2
2
H
1
2
6
P
1
6
7
M
1
7
9
E
1
8
0
L
1
8
1
I
1
8
2
E
1
8
6
D
2
1
8
Y
2
2
2
N
2
2
3
L
2
2
5
I
2
3
4
D
2
3
5
P
2
3
7
[1]1tqi.a . * . . . . . - . . . . . . . . . . . * .
[1]1tqm.a . . . . . . . - . . . . . . . . . . . . .
[1]1tqp.a * . . . . . . - . * . . . . . . . . . . .
[1]1zao.a . . . . . . . . . . . . . . . . . . . . .
[1]1zar.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
1tqi.a is apo
1tqm.a:anp
1tqp.a:atp
1zao.a:atp,mn
1zar.a:adp,mn
[1] 1tqi.a
-
1.9 1.8 4.0 1.8
[1] 1tqm.a -
0.2
0.1 0.6 0.3
[1] 1tqp.a - 0.1
0.1
0.5 0.2
[1] 1zao.a - 0.5 0.2
0.4
0.2
[1] 1zar.a - 0.5 0.3 0.8
0.3
[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
1tqi.a
1tqm.a
1tqp.a
1zao.a
1zar.a
[1] 1tqi.a
0
.18 .19 .21 .19
[1] 1tqm.a .18
0
0 .03 .03
[1] 1tqp.a .19 0
0
.03 .02
[1] 1zao.a .21 .03 .03
0
.02
[1] 1zar.a .19 .03 .02 .02
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
1tqi.a
1tqm.a
1tqp.a
1zao.a
1zar.a
[1] 1tqi.a
0
0.3 0.3 0.4 0.3
[1] 1tqm.a 0.3
0
0.1 0.4 0.3
[1] 1tqp.a 0.3 0.1
0
0.3 0.2
[1] 1zao.a 0.4 0.4 0.3
0
0.2
[1] 1zar.a 0.3 0.3 0.2 0.2
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

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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
1tqi.a
1tqm.a
1tqp.a
1zao.a
1zar.a
[1] 1tqi.a
0
1.1 1.1 1.1 1.1
[1] 1tqm.a 1.1
0
0.5 0.8 0.8
[1] 1tqp.a 1.1 0.5
0
0.8 0.8
[1] 1zao.a 1.1 0.8 0.8
0
0.3
[1] 1zar.a 1.1 0.8 0.8 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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