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PKNG_MYCTU_74_405

Serine/threonine-protein kinase PknG [Protein kinase superfamily. Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PKNG_MYCTU):D: Protein kinase (157, 158, 160:162, 165, 179, 181, 211, 232:237, 239, 276, 278, 280, 281, 283, 292, 293)
87, 92
87, 92, 157, 158, 160:162, 165, 179, 181, 211, 232:237, 239, 276, 278, 280, 281, 283, 292, 293
Metals (Me):Cd/Mg/Zn

Full PDB list

2pzi, 4y0x, 4y12

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
8
7
A
9
2
I
1
5
7
A
1
5
8
G
1
6
0
G
1
6
1
I
1
6
5
V
1
7
9
K
1
8
1
V
2
1
1
M
2
3
2
E
2
3
3
Y
2
3
4
V
2
3
5
G
2
3
6
G
2
3
7
M
2
8
3
I
2
9
2
D
2
9
3
[1]2pzi.b axx18 . . . . . . . . . . . . . . . . . . . Cd
[1]4y0x.a adp27 . . . . . . . . . . . . . . . . . . . Mg,Zn
[1]4y12.a ags31 . . . . . . . . . . . . . . . . . . . Mg,Zn

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

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PDB.ch
A1 Me
I
8
7
A
9
2
I
1
5
7
A
1
5
8
G
1
6
0
G
1
6
1
L
1
6
2
I
1
6
5
V
1
7
9
K
1
8
1
V
2
1
1
M
2
3
2
E
2
3
3
Y
2
3
4
V
2
3
5
G
2
3
6
G
2
3
7
S
2
3
9
D
2
7
6
K
2
7
8
E
2
8
0
N
2
8
1
M
2
8
3
I
2
9
2
D
2
9
3
[1]2pzi.b . . . . . . . . . . . . . . . . . . . . * . . . . Cd
[1]4y0x.a . . . . . . . . . . . . . . . . . . . . . . . . . Mg,Zn
[1]4y12.a . . . . . . . . . . . . . . . . . . . . . . . . . Mg,Zn

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
2pzi.b:axx
4y0x.a:adp
4y12.a:ags
[1] 2pzi.b
0
1.5 2.0
[1] 4y0x.a 0.1
0
0.2
[1] 4y12.a 0.1 0
0.2
[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
2pzi.b
4y0x.a
4y12.a
[1] 2pzi.b
0
.08 .08
[1] 4y0x.a .08
0
0
[1] 4y12.a .08 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
2pzi.b
4y0x.a
4y12.a
[1] 2pzi.b
0
3.1 3.1
[1] 4y0x.a 3.1
0
0.1
[1] 4y12.a 3.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2pzi.b
4y0x.a
4y12.a
[1] 2pzi.b
0
3.4 3.4
[1] 4y0x.a 3.4
0
0.2
[1] 4y12.a 3.4 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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