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BUD32_YEAST_1_261

EKC/KEOPS complex subunit BUD32 [Protein kinase superfamily. BUD32 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BUD32_YEAST):D: Protein kinase (22:25, 28, 30, 50, 52, 54, 72, 92, 107:109, 119, 181, 182, 184)22:25, 28, 30, 50, 52, 54, 72, 92, 107:109, 119, 181, 182, 184

Full PDB list

4ww5, 4ww7, 4ww9, 4wwa

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
2
S
2
3
V
3
0
I
5
0
K
5
2
R
7
2
P
9
2
E
1
0
7
F
1
0
8
L
1
0
9
F
1
1
9
I
1
8
1
D
1
8
2
G
1
8
4
[1]4ww5.a anp27 . . . . . . . . . . . . . .
[1]4ww7.a amp23 . . . . . . . . . . . . . .
[1]4ww9.a adp,mg28 . . . . . . . . . . . . . .
[1]4wwa.a none . . . . . . . . . . . . . .

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
I
2
2
S
2
3
Q
2
4
G
2
5
A
2
8
V
3
0
I
5
0
K
5
2
R
5
4
R
7
2
P
9
2
E
1
0
7
F
1
0
8
L
1
0
9
F
1
1
9
I
1
8
1
D
1
8
2
G
1
8
4
[1]4ww5.a . . . - . . . . . . . . . . . . * .
[1]4ww7.a . . . . . . . . . . . . . . . . * .
[1]4ww9.a . . . . . . . . . . . . . . . . * .
[1]4wwa.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
4ww5.a:anp
4ww7.a:amp
4ww9.a:adp,mg
4wwa.a is apo
[1] 4ww5.a
0.1
1.0 0.1 -
[1] 4ww7.a 1.4
0
0 -
[1] 4ww9.a 0.1 1.1
0.1
-
[1] 4wwa.a 2.3 0.1 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
4ww5.a
4ww7.a
4ww9.a
4wwa.a
[1] 4ww5.a
0
.02 .01 .08
[1] 4ww7.a .02
0
.02 .11
[1] 4ww9.a .01 .02
0
.09
[1] 4wwa.a .08 .11 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
4ww5.a
4ww7.a
4ww9.a
4wwa.a
[1] 4ww5.a
0
0.8 0.3 0.6
[1] 4ww7.a 0.8
0
0.9 0.9
[1] 4ww9.a 0.3 0.9
0
0.9
[1] 4wwa.a 0.6 0.9 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4ww5.a
4ww7.a
4ww9.a
4wwa.a
[1] 4ww5.a
0
1.2 0.3 1.0
[1] 4ww7.a 1.2
0
0.9 0.9
[1] 4ww9.a 0.3 0.9
0
1.1
[1] 4wwa.a 1.0 0.9 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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