If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

DCE1_HUMAN_92_594

Glutamate decarboxylase 1 [Group II decarboxylase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DCE1_HUMAN):R: Substrate binding (190:192)
189, 251:253, 256, 291, 344, 346, 348, 373, 375, 376, 402, 404, 405, 567
189:192, 251:253, 256, 291, 344, 346, 348, 373, 375, 376, 402, 404, 405, 567
A2 (DCE1_HUMAN):212, 214, 434, 435, 455, 456212, 214, 434, 435, 455, 456

Full PDB list

2okj, 3vp6

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
N
1
8
9
Q
1
9
0
L
1
9
1
S
1
9
2
G
2
5
1
G
2
5
2
A
2
5
3
H
2
9
1
T
3
4
4
G
3
4
6
T
3
4
8
D
3
7
3
A
3
7
5
W
3
7
6
N
4
0
2
H
4
0
4
K
4
0
5
R
5
6
7
F
2
1
4
Y
4
3
4
L
4
3
5
C
4
5
5
G
4
5
6
[1]2okj.a abu,plp22 . . . . . . . . . . . . . . . . * . . . . . .
[1]2okj.b abu,plp,plz44 . . . . . . . . . . . . . . . . * . . . . . .
[1]3vp6.b hld,plp28 . . . . . . . . . . . . . . . . * . . . . . .

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

[download in TSV format]
   
PDB.ch
A1 A2
N
1
8
9
Q
1
9
0
L
1
9
1
S
1
9
2
G
2
5
1
G
2
5
2
A
2
5
3
N
2
5
6
H
2
9
1
T
3
4
4
G
3
4
6
T
3
4
8
D
3
7
3
A
3
7
5
W
3
7
6
N
4
0
2
H
4
0
4
K
4
0
5
R
5
6
7
N
2
1
2
F
2
1
4
Y
4
3
4
L
4
3
5
C
4
5
5
G
4
5
6
[1]2okj.a . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2okj.b . . . . . . . . . . . . . . . . . * . . . . . . .
[1]3vp6.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2okj.a:abu,plp
2okj.b:abu,plp,plz
3vp6.b:hld,plp
[1] 2okj.a
0.8
0.6 0.9
[1] 2okj.b 0.8
0.6
1.0
[1] 3vp6.b 0.7 0.6
0.6
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2okj.a
2okj.b
3vp6.b
[1] 2okj.a
0
0 .02
[1] 2okj.b 0
0
.02
[1] 3vp6.b .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
2okj.a
2okj.b
3vp6.b
[1] 2okj.a
0
0.5 0.3
[1] 2okj.b 0.5
0
0.6
[1] 3vp6.b 0.3 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2okj.a
2okj.b
3vp6.b
[1] 2okj.a
0
0.7 0.7
[1] 2okj.b 0.7
0
0.8
[1] 3vp6.b 0.7 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...