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GCN2_YEAST_593_997_ATPsite

eIF-2-alpha kinase GCN2 [Protein kinase superfamily. Ser/Thr protein kinase family. GCN2 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (GCN2_YEAST):D: Protein kinase 2 (605:608, 612, 613, 626, 628, 656, 788:791, 835, 837, 840, 842, 853)605:608, 612, 613, 626, 628, 656, 788:791, 835, 837, 840, 842, 853

Full PDB list

1zxe, 1zy4, 1zy5, 1zyc, 1zyd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
6
0
5
G
6
0
6
Q
6
0
7
V
6
1
3
A
6
2
6
K
6
2
8
V
6
5
6
E
7
8
9
Y
7
9
0
C
7
9
1
D
8
3
5
K
8
3
7
N
8
4
0
F
8
4
2
D
8
5
3
[1]1zxe.a none . . . . . . . . . . N . . . .
[1]1zy4.b none . . . . . . . . . . . . . . .
[1]1zy5.a anp,mg32 . . . . . . . . . . . . . . .
[1]1zyd.a atp,mg,mg33 . . . . . . . . . . . . . . .
[1]1zyd.b atp,mg32 . . . . . . . . . . . . . . .

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
6
0
5
G
6
0
6
Q
6
0
7
G
6
0
8
Q
6
1
2
V
6
1
3
A
6
2
6
K
6
2
8
V
6
5
6
M
7
8
8
E
7
8
9
Y
7
9
0
C
7
9
1
D
8
3
5
K
8
3
7
N
8
4
0
F
8
4
2
D
8
5
3
[1]1zxe.a . . . . . . . . . * . . . N * . . .
[1]1zy4.b . . . . . . . . . . . . . * * . . *
[1]1zy5.a . . . . . . . . . . . . . * * . . .
[1]1zyd.a . . . . . . . . . . . . . . . . . .
[1]1zyd.b . . . . . . . . . . . . . . . . . .

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
1zxe.a is apo
1zy4.b is apo
1zy5.a:anp,mg
1zyd.a:atp,mg
1zyd.b:atp,mg
[1] 1zxe.a
-
- 1.2 1.5 1.6
[1] 1zy4.b -
-
0.9 2.3 3.0
[1] 1zy5.a - -
0
1.2 1.6
[1] 1zyd.a - - 0.2
0.2
0.1
[1] 1zyd.b - - 0.2 0.2
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
1zxe.a
1zy4.b
1zy5.a
1zyd.a
1zyd.b
[1] 1zxe.a
0
.16 .12 .16 .15
[1] 1zy4.b .16
0
.08 .16 .15
[1] 1zy5.a .12 .08
0
.10 .09
[1] 1zyd.a .16 .16 .10
0
.01
[1] 1zyd.b .15 .15 .09 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1zxe.a
1zy4.b
1zy5.a
1zyd.a
1zyd.b
[1] 1zxe.a
0
1.1 1.3 1.1 1.0
[1] 1zy4.b 1.1
0
0.7 1.2 1.1
[1] 1zy5.a 1.3 0.7
0
1.2 1.2
[1] 1zyd.a 1.1 1.2 1.2
0
0.4
[1] 1zyd.b 1.0 1.1 1.2 0.4
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
1zxe.a
1zy4.b
1zy5.a
1zyd.a
1zyd.b
[1] 1zxe.a
0
1.9 2.1 1.2 1.1
[1] 1zy4.b 1.9
0
0.8 2.0 1.9
[1] 1zy5.a 2.1 0.8
0
2.0 2.0
[1] 1zyd.a 1.2 2.0 2.0
0
0.6
[1] 1zyd.b 1.1 1.9 2.0 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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