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RIO1_ARCFU_1_258

RIO-type serine/threonine-protein kinase Rio1 [Protein kinase superfamily. RIO-type Ser/Thr kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RIO1_ARCFU):D: Protein kinase (55, 56, 60, 61, 63, 78, 80, 82, 135, 147:150, 156, 159, 201, 203, 211, 212)55, 56, 60, 61, 63, 78, 80, 82, 135, 147:150, 156, 159, 201, 203, 211, 212
Metals (Me):Mn

Full PDB list

1zp9, 1ztf, 1zth, 3re4, 4jin

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
5
5
S
5
6
A
6
1
V
6
3
A
7
8
K
8
0
Y
8
2
P
1
3
5
M
1
4
7
E
1
4
8
F
1
4
9
I
1
5
0
P
1
5
6
T
1
5
9
N
2
0
1
M
2
0
3
I
2
1
1
D
2
1
2
[1]1zp9.a atp31 . . . . . . . . * . . . . . . * . . Mn
[1]1ztf.a xya19 . . . . . . . . * . . . . . . * . .
[1]1zth.a adp27 . . . . . . . . * . . . . . . * . . Mn
[1]3re4.a to121 . . . . . . . . . . . . . . . . . .
[1]4jin.a 1l720 . . . . . . . . . . . . . . . . . .

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
5
5
S
5
6
E
6
0
A
6
1
V
6
3
A
7
8
K
8
0
Y
8
2
P
1
3
5
M
1
4
7
E
1
4
8
F
1
4
9
I
1
5
0
P
1
5
6
T
1
5
9
N
2
0
1
M
2
0
3
I
2
1
1
D
2
1
2
[1]1zp9.a . . . . . . . . . * . . . . . . * . . Mn
[1]1ztf.a . . . . . . . . . * . . . . . . * . .
[1]1zth.a . . . . . . . . . * . . . . . . * . . Mn
[1]3re4.a . . . . . . . . . . . . . . . . . . *
[1]4jin.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
1zp9.a:atp
1ztf.a:xya
1zth.a:adp
3re4.a:to1
4jin.a:1l7
[1] 1zp9.a
0.2
0 0.1 0 0.5
[1] 1ztf.a 0
0
0 0.2 0.2
[1] 1zth.a 0.2 0
0
0 0.5
[1] 3re4.a 1.5 0.2 1.3
0
1.0
[1] 4jin.a 0.2 0.1 0.3 0.5
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
1zp9.a
1ztf.a
1zth.a
3re4.a
4jin.a
[1] 1zp9.a
0
.05 0 .07 .06
[1] 1ztf.a .05
0
.05 .09 .02
[1] 1zth.a 0 .05
0
.07 .06
[1] 3re4.a .07 .09 .07
0
.10
[1] 4jin.a .06 .02 .06 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1zp9.a
1ztf.a
1zth.a
3re4.a
4jin.a
[1] 1zp9.a
0
0.7 0.1 0.2 0.8
[1] 1ztf.a 0.7
0
0.7 0.7 0.3
[1] 1zth.a 0.1 0.7
0
0.2 0.8
[1] 3re4.a 0.2 0.7 0.2
0
0.8
[1] 4jin.a 0.8 0.3 0.8 0.8
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
1zp9.a
1ztf.a
1zth.a
3re4.a
4jin.a
[1] 1zp9.a
0
1.1 0.3 0.7 1.0
[1] 1ztf.a 1.1
0
1.1 1.1 0.5
[1] 1zth.a 0.3 1.1
0
0.7 1.0
[1] 3re4.a 0.7 1.1 0.7
0
1.0
[1] 4jin.a 1.0 0.5 1.0 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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