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ACOX_SYNY3_1_490

Apocarotenoid-15,15'-oxygenase [Carotenoid oxygenase family]

Composition of the binding site

Protein chains monomer
A1 (ACOX_SYNY3):20, 69, 112, 113, 130, 136, 149:151, 205, 206, 234, 236, 238, 268, 269, 272, 303, 304, 322, 334, 342, 370, 371, 400, 48320, 69, 112, 113, 130, 136, 149:151, 205, 206, 234, 236, 238, 268, 269, 272, 303, 304, 322, 334, 342, 370, 371, 400, 483
Metals (Me):Fe

Full PDB list

2biw, 2bix, 4ou8, 4ou9, 5kja, 5kjb, 5kjd, 5kk0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
F
6
9
V
1
1
2
F
1
1
3
L
1
3
0
T
1
3
6
W
1
4
9
E
1
5
0
G
1
5
1
S
2
0
6
F
2
3
6
H
2
3
8
F
3
0
3
H
3
0
4
Y
3
2
2
F
3
3
4
E
3
7
0
F
3
7
1
L
4
0
0
L
4
8
3
[1]2biw.b 3on32 . . . . . . . . . . . . . . . . . . . Fe
[1]2bix.b c8e21 . . . . . . . . . . . . . . . . . . .
[1]4ou9.b none . . . . . . . . . . . . . . . . . . . Fe
[1]5kja.a none . . . . . A . . . . . . . . . . . . . Fe
[1]5kjb.a none . . . . . . D . . . . . . . . . . . . Fe
[1]5kjd.c none . . . . . . Q . . . . . . . . . . . . Fe
[1]5kk0.a none . . . . A . . . . . . . . . . . . . . Fe

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 Me
W
2
0
F
6
9
V
1
1
2
F
1
1
3
L
1
3
0
T
1
3
6
W
1
4
9
E
1
5
0
G
1
5
1
K
2
0
5
S
2
0
6
F
2
3
4
F
2
3
6
H
2
3
8
A
2
6
8
G
2
6
9
V
2
7
2
F
3
0
3
H
3
0
4
Y
3
2
2
F
3
3
4
L
3
4
2
E
3
7
0
F
3
7
1
L
4
0
0
L
4
8
3
[1]2biw.b . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]2bix.b . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ou9.b . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]5kja.a . . . . . . A . . . . . . . . . . * . . . . . . . . Fe
[1]5kjb.a . . . . . . . D . . . . . . . . . * . . . . . . . . Fe
[1]5kjd.c . * . . . . . Q . . . . . . . . . * . . . . . . . . Fe
[1]5kk0.a . . . . . A . . . . . . . . . . . . . . . . . . . . Fe

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
2biw.b:3on
2bix.b:c8e
4ou9.b is apo
5kja.a is apo
5kjb.a is apo
5kjd.c is apo
5kk0.a is apo
[1] 2biw.b
0.3
0 - - - - -
[1] 2bix.b 0.7
0
- - - - -
[1] 4ou9.b 0.3 0
-
- - - -
[1] 5kja.a 1.3 0.4 -
-
- - -
[1] 5kjb.a 1.2 0 - -
-
- -
[1] 5kjd.c 4.3 2.1 - - -
-
-
[1] 5kk0.a 0.7 0 - - - -
-
[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
2biw.b
2bix.b
4ou9.b
5kja.a
5kjb.a
5kjd.c
5kk0.a
[1] 2biw.b
0
.03 .01 .06 .03 .16 .01
[1] 2bix.b .03
0
.01 .03 .02 .13 .02
[1] 4ou9.b .01 .01
0
.04 .03 .15 .01
[1] 5kja.a .06 .03 .04
0
.03 .13 .04
[1] 5kjb.a .03 .02 .03 .03
0
.12 .03
[1] 5kjd.c .16 .13 .15 .13 .12
0
.14
[1] 5kk0.a .01 .02 .01 .04 .03 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
2biw.b
2bix.b
4ou9.b
5kja.a
5kjb.a
5kjd.c
5kk0.a
[1] 2biw.b
0
0.5 0.3 0.9 0.5 0.6 0.4
[1] 2bix.b 0.5
0
0.5 0.8 0.5 0.4 0.5
[1] 4ou9.b 0.3 0.5
0
0.8 0.3 0.5 0.3
[1] 5kja.a 0.9 0.8 0.8
0
0.6 0.6 0.8
[1] 5kjb.a 0.5 0.5 0.3 0.6
0
0.3 0.3
[1] 5kjd.c 0.6 0.4 0.5 0.6 0.3
0
0.5
[1] 5kk0.a 0.4 0.5 0.3 0.8 0.3 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2biw.b
2bix.b
4ou9.b
5kja.a
5kjb.a
5kjd.c
5kk0.a
[1] 2biw.b
0
1.0 0.7 1.2 1.1 1.1 0.8
[1] 2bix.b 1.0
0
1.0 1.2 1.1 1.1 1.1
[1] 4ou9.b 0.7 1.0
0
1.1 1.0 1.0 0.6
[1] 5kja.a 1.2 1.2 1.1
0
0.9 0.9 1.0
[1] 5kjb.a 1.1 1.1 1.0 0.9
0
0.9 1.0
[1] 5kjd.c 1.1 1.1 1.0 0.9 0.9
0
1.0
[1] 5kk0.a 0.8 1.1 0.6 1.0 1.0 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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