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ADAS_CAVPO_15_658

Alkyldihydroxyacetonephosphate synthase, peroxisomal [FAD-binding oxidoreductase/transferase type 4 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ADAS_CAVPO):D: FAD-binding PCMH-type (233:241, 244, 245, 260, 280, 302:304, 308, 309, 311:313, 315, 316, 318, 319, 368, 369, 372:374)
R: Important for enzyme activity (616, 617)
96, 128, 131, 132, 136, 189, 419, 421, 425, 426, 428, 429, 467, 503:508, 511, 512, 514, 515, 517, 518, 523:527, 562, 564, 566, 578, 580:582, 654, 656
96, 128, 131, 132, 136, 189, 233:241, 244, 245, 260, 280, 302:304, 308, 309, 311:313, 315, 316, 318, 319, 368, 369, 372:374, 419, 421, 425, 426, 428, 429, 467, 503:508, 511, 512, 514, 515, 517, 518, 523:527, 562, 564, 566, 578, 580:582, 616, 617, 654, 656

Full PDB list

4bby, 4bc7, 4bc9, 4bca, 5adz, 5ae1, 5ae2, 5ae3

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
9
6
F
1
2
8
W
1
3
1
I
1
3
2
F
1
3
6
H
1
8
9
P
2
3
4
I
2
3
5
G
2
3
6
G
2
3
7
G
2
3
8
T
2
3
9
S
2
4
0
V
2
4
1
G
2
4
4
L
2
4
5
T
2
6
0
P
3
0
2
D
3
0
3
S
3
0
4
S
3
0
8
T
3
0
9
G
3
1
1
G
3
1
2
W
3
1
3
S
3
1
5
T
3
1
6
A
3
1
8
S
3
1
9
E
3
6
8
G
3
6
9
G
3
7
2
V
3
7
3
I
3
7
4
R
4
1
9
M
4
2
1
Q
4
2
5
F
4
2
8
G
4
2
9
T
4
6
7
G
5
0
4
L
5
0
7
I
5
1
1
A
5
1
2
M
5
1
4
R
5
1
5
G
5
1
8
I
5
2
3
G
5
2
5
E
5
2
6
S
5
2
7
R
5
6
6
Y
5
7
8
Y
5
8
0
F
5
8
1
A
5
8
2
H
6
1
6
H
6
1
7
N
6
5
4
N
6
5
6
[1]4bby.a fad53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bc7.b 1do,fad66 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bc7.d fad53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bc9.a cnv.fad57 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bca.a fad53 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . F . . . . . . .
[1]5adz.a fad,kqs77 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ae1.a b2z,fad78 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ae2.b fad,fyc77 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ae3.b awb,fad92 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
W
9
6
F
1
2
8
W
1
3
1
I
1
3
2
F
1
3
6
H
1
8
9
I
2
3
3
P
2
3
4
I
2
3
5
G
2
3
6
G
2
3
7
G
2
3
8
T
2
3
9
S
2
4
0
V
2
4
1
G
2
4
4
L
2
4
5
T
2
6
0
A
2
8
0
P
3
0
2
D
3
0
3
S
3
0
4
S
3
0
8
T
3
0
9
G
3
1
1
G
3
1
2
W
3
1
3
S
3
1
5
T
3
1
6
A
3
1
8
S
3
1
9
E
3
6
8
G
3
6
9
G
3
7
2
V
3
7
3
I
3
7
4
R
4
1
9
M
4
2
1
Q
4
2
5
F
4
2
6
F
4
2
8
G
4
2
9
T
4
6
7
R
5
0
3
G
5
0
4
Y
5
0
5
L
5
0
6
L
5
0
7
T
5
0
8
I
5
1
1
A
5
1
2
M
5
1
4
R
5
1
5
L
5
1
7
G
5
1
8
I
5
2
3
I
5
2
4
G
5
2
5
E
5
2
6
S
5
2
7
L
5
6
2
T
5
6
4
R
5
6
6
Y
5
7
8
Y
5
8
0
F
5
8
1
A
5
8
2
H
6
1
6
H
6
1
7
N
6
5
4
N
6
5
6
[1]4bby.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4bc7.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . H . . . * . . . * . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]4bc7.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . H . . . * . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4bc9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4bca.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . F * . . . . . .
[1]5adz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ae1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ae2.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ae3.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
4bby.a:fad
4bc7.b:1do,fad
4bc7.d:fad
4bc9.a:cnv.fad
4bca.a:fad
5adz.a:fad,kqs
5ae1.a:b2z,fad
5ae2.b:fad,fyc
5ae3.b:awb,fad
[1] 4bby.a
0
2.8 0 0.6 0.1 2.5 2.6 3.4 6.4
[1] 4bc7.b 0.2
0
0.1 0.8 0.2 1.3 1.3 1.1 8.0
[1] 4bc7.d 0.1 2.8
0
0.8 0.2 3.1 3.1 3.7 6.6
[1] 4bc9.a 0.1 2.2 0
0.3
0.1 2.2 2.2 2.8 6.9
[1] 4bca.a 0.3 2.7 0.1 0.9
0.1
2.7 2.8 3.2 6.3
[1] 5adz.a 0.1 0.1 0 0.8 0.1
0
0.1 0.2 3.0
[1] 5ae1.a 0.1 0.2 0 0.4 0.2 0.1
0.1
0.2 3.3
[1] 5ae2.b 0.2 0.2 0.1 0.7 0.2 0.2 0.2
0.2
4.2
[1] 5ae3.b 0.1 0 0 0.9 0.1 1.6 1.2 1.0
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
4bby.a
4bc7.b
4bc7.d
4bc9.a
4bca.a
5adz.a
5ae1.a
5ae2.b
5ae3.b
[1] 4bby.a
0
.14 .03 .03 .02 .06 .06 .07 .11
[1] 4bc7.b .14
0
.13 .13 .13 .10 .11 .08 .12
[1] 4bc7.d .03 .13
0
.04 .03 .08 .08 .09 .11
[1] 4bc9.a .03 .13 .04
0
.03 .07 .06 .07 .12
[1] 4bca.a .02 .13 .03 .03
0
.06 .06 .07 .11
[1] 5adz.a .06 .10 .08 .07 .06
0
.01 .03 .07
[1] 5ae1.a .06 .11 .08 .06 .06 .01
0
.04 .08
[1] 5ae2.b .07 .08 .09 .07 .07 .03 .04
0
.08
[1] 5ae3.b .11 .12 .11 .12 .11 .07 .08 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
4bby.a
4bc7.b
4bc7.d
4bc9.a
4bca.a
5adz.a
5ae1.a
5ae2.b
5ae3.b
[1] 4bby.a
0
0.9 0.4 0.3 0.2 0.2 0.2 0.4 0.7
[1] 4bc7.b 0.9
0
0.9 0.9 1.0 0.9 0.9 0.9 1.0
[1] 4bc7.d 0.4 0.9
0
0.3 0.3 0.4 0.4 0.4 0.7
[1] 4bc9.a 0.3 0.9 0.3
0
0.3 0.3 0.3 0.3 0.6
[1] 4bca.a 0.2 1.0 0.3 0.3
0
0.3 0.3 0.3 0.7
[1] 5adz.a 0.2 0.9 0.4 0.3 0.3
0
0.1 0.3 0.7
[1] 5ae1.a 0.2 0.9 0.4 0.3 0.3 0.1
0
0.3 0.6
[1] 5ae2.b 0.4 0.9 0.4 0.3 0.3 0.3 0.3
0
0.6
[1] 5ae3.b 0.7 1.0 0.7 0.6 0.7 0.7 0.6 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

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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
4bby.a
4bc7.b
4bc7.d
4bc9.a
4bca.a
5adz.a
5ae1.a
5ae2.b
5ae3.b
[1] 4bby.a
0
1.2 0.8 0.6 0.5 0.7 0.8 0.8 1.2
[1] 4bc7.b 1.2
0
1.2 1.3 1.2 1.1 1.1 1.1 1.2
[1] 4bc7.d 0.8 1.2
0
0.7 0.7 0.9 0.9 0.9 1.1
[1] 4bc9.a 0.6 1.3 0.7
0
0.6 0.8 0.8 0.9 1.1
[1] 4bca.a 0.5 1.2 0.7 0.6
0
0.8 0.8 0.7 1.1
[1] 5adz.a 0.7 1.1 0.9 0.8 0.8
0
0.4 0.6 0.9
[1] 5ae1.a 0.8 1.1 0.9 0.8 0.8 0.4
0
0.6 0.9
[1] 5ae2.b 0.8 1.1 0.9 0.9 0.7 0.6 0.6
0
0.9
[1] 5ae3.b 1.2 1.2 1.1 1.1 1.1 0.9 0.9 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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