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RK_BOVIN_30_535

Rhodopsin kinase [Protein kinase superfamily. AGC Ser/Thr protein kinase family. GPRK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RK_BOVIN):D: Protein kinase (191:201, 214, 216, 248, 264:268, 270, 271, 318, 319, 321, 331, 332)191:201, 214, 216, 248, 264:268, 270, 271, 318, 319, 321, 331, 332, 474:478, 481
Metals (Me):Mg

Full PDB list

3c4w, 3c4x, 3c4z, 3c50, 3qc9, 3t8o, 4l9i, 4pni, 4wbo (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
L
1
9
3
G
1
9
4
R
1
9
5
G
1
9
6
G
1
9
7
F
1
9
8
G
1
9
9
V
2
0
1
A
2
1
4
K
2
1
6
V
2
4
8
M
2
6
4
T
2
6
5
I
2
6
6
M
2
6
7
N
2
6
8
G
2
7
0
D
2
7
1
E
3
1
8
N
3
1
9
L
3
2
1
S
3
3
1
D
3
3
2
R
4
7
4
T
4
7
5
Y
4
7
7
A
4
7
8
[1]3c4w.b atp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3c4x.a atp31 . . . . . . . . . . . . . . . . . . . . . . . - - - - Mg
[1]3c4z.a adp,mg28 . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]4l9i.b 8pr24 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4pni.a kqq39 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wbo.d anw22 . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
R
1
9
1
V
1
9
2
L
1
9
3
G
1
9
4
R
1
9
5
G
1
9
6
G
1
9
7
F
1
9
8
G
1
9
9
E
2
0
0
V
2
0
1
A
2
1
4
K
2
1
6
V
2
4
8
M
2
6
4
T
2
6
5
I
2
6
6
M
2
6
7
N
2
6
8
G
2
7
0
D
2
7
1
E
3
1
8
N
3
1
9
L
3
2
1
S
3
3
1
D
3
3
2
R
4
7
4
T
4
7
5
V
4
7
6
Y
4
7
7
A
4
7
8
I
4
8
1
[1]3c4w.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - Mg
[1]3c4x.a . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - . Mg
[1]3c4z.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - Mg
[1]4l9i.b . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4pni.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wbo.d . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .

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
3c4w.b:atp,mg
3c4x.a:atp
3c4z.a:adp,mg
4l9i.b:8pr
4pni.a:kqq
4wbo.d:anw
[1] 3c4w.b
0.2
0.3 0.2 0.3 1.8 0.7
[1] 3c4x.a 0.1
0.1
0 0.6 1.8 0.6
[1] 3c4z.a 0.1 0.1
0.1
0.6 2.0 0.7
[1] 4l9i.b 0.3 0.5 0.2
0
2.7 1.5
[1] 4pni.a 1.7 1.4 1.3 1.8
0
0
[1] 4wbo.d 1.5 1.6 1.1 0.8 0.4
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
3c4w.b
3c4x.a
3c4z.a
4l9i.b
4pni.a
4wbo.d
[1] 3c4w.b
0
.06 .03 .05 .13 .11
[1] 3c4x.a .06
0
.05 .10 .12 .12
[1] 3c4z.a .03 .05
0
.08 .13 .11
[1] 4l9i.b .05 .10 .08
0
.15 .13
[1] 4pni.a .13 .12 .13 .15
0
.02
[1] 4wbo.d .11 .12 .11 .13 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
3c4w.b
3c4x.a
3c4z.a
4l9i.b
4pni.a
4wbo.d
[1] 3c4w.b
0
0.3 0.3 0.9 3.1 1.3
[1] 3c4x.a 0.3
0
0.4 0.8 2.5 1.8
[1] 3c4z.a 0.3 0.4
0
0.8 3.1 1.3
[1] 4l9i.b 0.9 0.8 0.8
0
3.0 1.3
[1] 4pni.a 3.1 2.5 3.1 3.0
0
3.7
[1] 4wbo.d 1.3 1.8 1.3 1.3 3.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
3c4w.b
3c4x.a
3c4z.a
4l9i.b
4pni.a
4wbo.d
[1] 3c4w.b
0
0.6 0.8 1.3 4.3 1.9
[1] 3c4x.a 0.6
0
0.9 1.3 3.3 2.3
[1] 3c4z.a 0.8 0.9
0
1.6 4.5 2.1
[1] 4l9i.b 1.3 1.3 1.6
0
4.2 1.9
[1] 4pni.a 4.3 3.3 4.5 4.2
0
4.4
[1] 4wbo.d 1.9 2.3 2.1 1.9 4.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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