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YPKA_YERPS_90_433

Protein kinase YpkA [Protein kinase superfamily. Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (YPKA_YERPS):D: Protein kinase (147, 149, 161, 163, 166, 214:217, 221, 274, 275, 288, 289)147, 149, 161, 163, 166, 214:217, 221, 274, 275, 288, 289
Metals (Me):Mg

Full PDB list

4ci6, 5ce3

Pocket contact map

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PDB.ch
   
ligand
A1 Me
S
1
4
7
I
1
4
9
V
1
6
1
K
1
6
3
R
1
6
6
M
2
1
4
D
2
1
5
E
2
1
6
V
2
1
7
R
2
2
1
G
2
7
4
N
2
7
5
I
2
8
8
D
2
8
9
[1]4ci6.b none - . . . - . . . . . . . . .
[1]5ce3.b adp27 . . . . . . . . . . . . . . Mg

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
S
1
4
7
I
1
4
9
V
1
6
1
K
1
6
3
R
1
6
6
M
2
1
4
D
2
1
5
E
2
1
6
V
2
1
7
R
2
2
1
G
2
7
4
N
2
7
5
I
2
8
8
D
2
8
9
[1]4ci6.b - . . . - . . . . . . . . .
[1]5ce3.b . . . . . . . . . . . . . . Mg

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
4ci6.b is apo
5ce3.b:adp
[1] 4ci6.b
-
0.3
[1] 5ce3.b -
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
4ci6.b
5ce3.b
[1] 4ci6.b
0
.03
[1] 5ce3.b .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
4ci6.b
5ce3.b
[1] 4ci6.b
0
0.9
[1] 5ce3.b 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
4ci6.b
5ce3.b
[1] 4ci6.b
0
1.0
[1] 5ce3.b 1.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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