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AOC2_ARATH_73_253

Allene oxide cyclase 2, chloroplastic [Allene oxide cyclase family]

Composition of the binding site

Protein chains monomer
A1 (AOC2_ARATH):88, 90, 97, 99, 108, 114, 116, 118, 136, 150, 152, 154, 170, 196, 201:205, 20788, 90, 97, 99, 108, 114, 116, 118, 136, 150, 152, 154, 170, 196, 201:205, 207

Full PDB list

1z8k, 2brj, 2dio, 2gin, 2q4i, 4cq6, 4cq7 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
8
8
N
9
0
P
9
7
I
9
9
F
1
0
8
V
1
1
4
F
1
1
6
N
1
1
8
C
1
3
6
F
1
5
0
A
1
5
2
Y
1
5
4
Y
1
7
0
L
1
9
6
Y
2
0
1
P
2
0
2
T
2
0
3
L
2
0
5
Y
2
0
7
[1]2brj.b none . . . . . . . . . . . . . . . . . . .
[1]2dio.b eod21 . . . . . . . . . . . . . . . . . . .
[1]4cq6.b t2521 . . . . . . . . . . . . . . . . . . .
[1]4cq7.a whw21 . . . . . . . . . . . . . . . . . . .
[1]4cq7.c mrd8 . . . . . . . . . . . . . . . . . . .

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
E
8
8
N
9
0
P
9
7
I
9
9
F
1
0
8
V
1
1
4
F
1
1
6
N
1
1
8
C
1
3
6
F
1
5
0
A
1
5
2
Y
1
5
4
Y
1
7
0
L
1
9
6
Y
2
0
1
P
2
0
2
T
2
0
3
K
2
0
4
L
2
0
5
Y
2
0
7
[1]2brj.b . . . . . . . . . . . . . . . * . . . .
[1]2dio.b . . . . . . . . . . . . . . . * . . . .
[1]4cq6.b . . . . . . . . . . . . . . . * . . . .
[1]4cq7.a . . . . . . . . . . . . * . . . . . . .
[1]4cq7.c . . . . . . . . . . . . . . . . . . . .

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
2brj.b is apo
2dio.b:eod
4cq6.b:t25
4cq7.a:whw
4cq7.c:mrd
[1] 2brj.b
-
0 0 1.0 0
[1] 2dio.b -
0
0 1.0 0
[1] 4cq6.b - 0
0
1.0 0
[1] 4cq7.a - 2.0 1.7
0
1.4
[1] 4cq7.c - 0 0 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
2brj.b
2dio.b
4cq6.b
4cq7.a
4cq7.c
[1] 2brj.b
0
0 0 .15 .01
[1] 2dio.b 0
0
0 .15 .01
[1] 4cq6.b 0 0
0
.15 .01
[1] 4cq7.a .15 .15 .15
0
.14
[1] 4cq7.c .01 .01 .01 .14
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
2brj.b
2dio.b
4cq6.b
4cq7.a
4cq7.c
[1] 2brj.b
0
0.1 0.1 0.4 0.3
[1] 2dio.b 0.1
0
0.1 0.4 0.3
[1] 4cq6.b 0.1 0.1
0
0.4 0.3
[1] 4cq7.a 0.4 0.4 0.4
0
0.4
[1] 4cq7.c 0.3 0.3 0.3 0.4
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
2brj.b
2dio.b
4cq6.b
4cq7.a
4cq7.c
[1] 2brj.b
0
0.2 0.7 0.8 0.6
[1] 2dio.b 0.2
0
0.7 0.8 0.6
[1] 4cq6.b 0.7 0.7
0
0.8 0.5
[1] 4cq7.a 0.8 0.8 0.8
0
0.7
[1] 4cq7.c 0.6 0.6 0.5 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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