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PHO85_YEAST_6_305_ATPsite

Cyclin-dependent protein kinase PHO85 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PHO85_YEAST):D: Protein kinase (13:18, 21, 34, 36, 82:85, 88, 91, 133, 135, 137, 138, 140, 151)13:18, 21, 34, 36, 82:85, 88, 91, 133, 135, 137, 138, 140, 151

Full PDB list

2pk9, 2pmi, 4krc, 4krd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
3
N
1
5
G
1
6
T
1
7
V
2
1
A
3
4
K
3
6
F
8
2
E
8
3
M
8
5
D
8
8
K
1
3
5
Q
1
3
7
N
1
3
8
L
1
4
0
D
1
5
1
[1]2pmi.a ags31 - - - - . . . . . . . . . . . .
[1]4krc.a ags,mg32 . . . . . . . . . . . . . . . .
[1]4krd.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
L
1
3
G
1
4
N
1
5
G
1
6
T
1
7
Y
1
8
V
2
1
A
3
4
K
3
6
F
8
2
E
8
3
F
8
4
M
8
5
D
8
8
K
9
1
D
1
3
3
K
1
3
5
Q
1
3
7
N
1
3
8
L
1
4
0
D
1
5
1
[1]2pmi.a - - - - - - . . . . . . . . . . . . . . .
[1]4krc.a * . . . . . . . . . . . . . . . . . . . .
[1]4krd.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
2pmi.a:ags
4krc.a:ags,mg
4krd.a is apo
[1] 2pmi.a
0
0.6 -
[1] 4krc.a 3.0
0.3
-
[1] 4krd.a 1.4 0.4
-
[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
2pmi.a
4krc.a
4krd.a
[1] 2pmi.a
0
.14 .06
[1] 4krc.a .14
0
.10
[1] 4krd.a .06 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2pmi.a
4krc.a
4krd.a
[1] 2pmi.a
0
1.1 0.8
[1] 4krc.a 1.1
0
0.6
[1] 4krd.a 0.8 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2pmi.a
4krc.a
4krd.a
[1] 2pmi.a
0
1.3 1.2
[1] 4krc.a 1.3
0
0.9
[1] 4krd.a 1.2 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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