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DHE3_HUMAN_59_558

Glutamate dehydrogenase 1, mitochondrial [Glu/Leu/Phe/Val dehydrogenases family]

Composition of the binding site

Protein chains monomer
A1 (DHE3_HUMAN):207, 211, 243, 244, 246, 247207, 211, 243, 244, 246, 247

Full PDB list

1hwy, 1hwz, 1l1f, 1nr1, 3etd, 3ete, 3etg, 3mvo, 3mvq, 3mw9 (redundant Pocketome entry); 3jcz, 3jd0, 3jd1, 3jd2, 3jd4, 5k12 (unprocessed)

Pocket contact map

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PDB.ch
   
ligand
A1
T
2
4
3
I
2
4
4
Y
2
4
7
[1]3ete.a h3p21 . . .
[1]3mw9.d 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
M
2
0
7
K
2
1
1
T
2
4
3
I
2
4
4
H
2
4
6
Y
2
4
7
[1]3ete.a . . . . . .
[1]3mw9.d . . . . . .

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
3ete.a:h3p
3mw9.d is apo
[1] 3ete.a
0.1
-
[1] 3mw9.d 0.3
-
[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
3ete.a
3mw9.d
[1] 3ete.a
0
.03
[1] 3mw9.d .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3ete.a
3mw9.d
[1] 3ete.a
0
0.2
[1] 3mw9.d 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
3ete.a
3mw9.d
[1] 3ete.a
0
0.9
[1] 3mw9.d 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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