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.

BCKD_RAT_31_412

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial [PDK/BCKDK protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BCKD_RAT):D: Histidine kinase (159, 162, 165, 196, 197, 200, 201, 204)
98, 101, 102, 105, 129, 132, 136, 155, 158
98, 101, 102, 105, 129, 132, 136, 155, 158, 159, 162, 165, 196, 197, 200, 201, 204

Full PDB list

1gjv, 1gkx, 1gkz, 3tz0, 3tz2, 3tz4, 3tz5, 3vad, 4dzy, 4e00, 4e01, 4e02, 4h7q, 4h81, 4h85 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
9
8
R
1
0
1
I
1
0
2
R
1
0
5
Y
1
2
9
A
1
3
2
L
1
3
6
V
1
5
5
L
1
5
8
L
1
5
9
H
1
6
2
V
1
6
5
S
1
9
6
R
1
9
7
I
2
0
0
R
2
0
1
A
2
0
4
[1]3tz4.a 03h9 . . . . . . . . . . . . . . . . .
[1]3tz5.a clt12 . . . . . . . . . . . . . . . . .
[1]3vad.a 0f1,0f128 . . . . . . . . . . . . . . F . .
[1]4dzy.a wj112 . . . . . . . . . . . . . . . . .
[1]4e01.a 0f114 . . . . . . . . . . . . . . . . .
[1]4h7q.a none . . . . . . . . . . . . . . . . .
[1]4h81.a wj212 . . . . . . . . . . . . . . . . .
[1]4h85.a hri9 . . . . . . . . . . . . . . . . .

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
L
9
8
R
1
0
1
I
1
0
2
R
1
0
5
Y
1
2
9
A
1
3
2
L
1
3
6
V
1
5
5
L
1
5
8
L
1
5
9
H
1
6
2
V
1
6
5
S
1
9
6
R
1
9
7
I
2
0
0
R
2
0
1
A
2
0
4
[1]3tz4.a . . . . . . . . . . . . . . . . .
[1]3tz5.a . . . . . . . . . . . . . . * . .
[1]3vad.a . . . . . . . . . . . . . . F . .
[1]4dzy.a . . . . . . . . . . . . . . * . .
[1]4e01.a . . . . . . . . . . . . . . * . .
[1]4h7q.a . . . . . . . . . . . . . . * . .
[1]4h81.a . . . . . . . . . . . . . . * . .
[1]4h85.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3tz4.a:03h
3tz5.a:clt
3vad.a:0f1
4dzy.a:wj1
4e01.a:0f1
4h7q.a is apo
4h81.a:wj2
4h85.a:hri
[1] 3tz4.a
0
0 1.6 0 0.3 - 0 0
[1] 3tz5.a 0.1
0
1.8 0.1 0.2 - 0.1 0
[1] 3vad.a 0.4 0
1.9
0.1 0 - 0.1 0.3
[1] 4dzy.a 0 0 1.5
0
0.3 - 0.1 0.1
[1] 4e01.a 0.1 0 1.3 0.2
0
- 0.1 0.1
[1] 4h7q.a 0 0 2.1 0.1 0.4
-
0.2 0.1
[1] 4h81.a 0 0 1.7 0 0.3 -
0
0
[1] 4h85.a 0 0 2.0 0.1 0.4 - 0
0.1
[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
3tz4.a
3tz5.a
3vad.a
4dzy.a
4e01.a
4h7q.a
4h81.a
4h85.a
[1] 3tz4.a
0
.05 .15 .04 .08 .03 .03 .02
[1] 3tz5.a .05
0
.11 .03 .04 .04 .02 .04
[1] 3vad.a .15 .11
0
.11 .08 .14 .12 .14
[1] 4dzy.a .04 .03 .11
0
.06 .04 .01 .03
[1] 4e01.a .08 .04 .08 .06
0
.07 .05 .06
[1] 4h7q.a .03 .04 .14 .04 .07
0
.02 .01
[1] 4h81.a .03 .02 .12 .01 .05 .02
0
.02
[1] 4h85.a .02 .04 .14 .03 .06 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
3tz4.a
3tz5.a
3vad.a
4dzy.a
4e01.a
4h7q.a
4h81.a
4h85.a
[1] 3tz4.a
0
0.2 0.4 0.2 0.3 0.1 0.1 0.1
[1] 3tz5.a 0.2
0
0.3 0.1 0.2 0.2 0.2 0.2
[1] 3vad.a 0.4 0.3
0
0.3 0.3 0.4 0.4 0.4
[1] 4dzy.a 0.2 0.1 0.3
0
0.3 0.2 0.2 0.2
[1] 4e01.a 0.3 0.2 0.3 0.3
0
0.4 0.4 0.4
[1] 4h7q.a 0.1 0.2 0.4 0.2 0.4
0
0.1 0.1
[1] 4h81.a 0.1 0.2 0.4 0.2 0.4 0.1
0
0.1
[1] 4h85.a 0.1 0.2 0.4 0.2 0.4 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
3tz4.a
3tz5.a
3vad.a
4dzy.a
4e01.a
4h7q.a
4h81.a
4h85.a
[1] 3tz4.a
0
0.5 0.9 0.2 0.6 0.2 0.2 0.1
[1] 3tz5.a 0.5
0
0.9 0.5 0.5 0.6 0.6 0.5
[1] 3vad.a 0.9 0.9
0
0.9 0.9 1.0 0.9 0.9
[1] 4dzy.a 0.2 0.5 0.9
0
0.6 0.3 0.3 0.2
[1] 4e01.a 0.6 0.5 0.9 0.6
0
0.6 0.6 0.6
[1] 4h7q.a 0.2 0.6 1.0 0.3 0.6
0
0.2 0.1
[1] 4h81.a 0.2 0.6 0.9 0.3 0.6 0.2
0
0.2
[1] 4h85.a 0.1 0.5 0.9 0.2 0.6 0.1 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...