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CP74A_ARATH_31_518

Allene oxide synthase, chloroplastic [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP74A_ARATH):137, 138, 247, 251, 254, 255, 320, 321, 324, 325, 328, 388:390, 504137, 138, 247, 251, 254, 255, 320, 321, 324, 325, 328, 388:390, 504
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2rch, 2rcl, 2rcm, 3cli, 3dsi, 3dsj, 3dsk

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
F
1
3
7
T
1
3
8
V
2
4
7
L
2
5
1
L
2
5
4
F
3
2
0
N
3
2
1
G
3
2
4
G
3
2
5
I
3
2
8
V
3
8
8
T
3
8
9
A
3
9
0
L
5
0
4
[1]2rch.a 24321 . . . . . . . . . . . . . . hem Fe
[1]2rcl.a t2521 . . . . . . . . . . . . . . hem Fe
[1]2rcm.a none L . . . . . . . . . . . . . Fe
[1]3cli.a none . . . . . . . . . . . . . . hem Fe
[1]3dsi.a t2421 . . . . . . . . . . . . . . hem Fe
[1]3dsj.a 24321 L . . . . . . . . . . . . . Fe
[1]3dsk.a t2521 L . . . . . . . . . . . . . hem 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 cF Me
F
1
3
7
T
1
3
8
V
2
4
7
L
2
5
1
L
2
5
4
L
2
5
5
F
3
2
0
N
3
2
1
G
3
2
4
G
3
2
5
I
3
2
8
V
3
8
8
T
3
8
9
A
3
9
0
L
5
0
4
[1]2rch.a . . . . . . . . . . . . . . . hem Fe
[1]2rcl.a . . . . . . . . . . . . . . . hem Fe
[1]2rcm.a L . . . . . . . . . . . . . . Fe
[1]3cli.a . . . . . . . . . . . . . . . hem Fe
[1]3dsi.a . . . . . . . . . . . . . . . hem Fe
[1]3dsj.a L . . . . . . . . . . . . . . Fe
[1]3dsk.a L . . . . . . . . . . . . . . hem 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
2rch.a:243
2rcl.a:t25
2rcm.a is apo
3cli.a is apo
3dsi.a:t24
3dsj.a:243
3dsk.a:t25
[1] 2rch.a
0
0 - - 0 0 0.2
[1] 2rcl.a 0
0
- - 0 0 0.2
[1] 2rcm.a 0 0.1
-
- 0.1 0.1 0
[1] 3cli.a 0 0 -
-
0 0 0.2
[1] 3dsi.a 0 0 - -
0
0 0.2
[1] 3dsj.a 0 0.1 - - 0
0
0.1
[1] 3dsk.a 0 0 - - 0 0
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
2rch.a
2rcl.a
2rcm.a
3cli.a
3dsi.a
3dsj.a
3dsk.a
[1] 2rch.a
0
0 .03 0 0 .02 .01
[1] 2rcl.a 0
0
.03 0 0 .02 .01
[1] 2rcm.a .03 .03
0
.03 .03 .01 .01
[1] 3cli.a 0 0 .03
0
0 .02 .01
[1] 3dsi.a 0 0 .03 0
0
.02 .01
[1] 3dsj.a .02 .02 .01 .02 .02
0
.01
[1] 3dsk.a .01 .01 .01 .01 .01 .01
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
2rch.a
2rcl.a
2rcm.a
3cli.a
3dsi.a
3dsj.a
3dsk.a
[1] 2rch.a
0
0.2 0.6 0.2 0.6 0.6 0.6
[1] 2rcl.a 0.2
0
0.5 0.2 0.6 0.6 0.7
[1] 2rcm.a 0.6 0.5
0
0.5 0.3 0.3 0.3
[1] 3cli.a 0.2 0.2 0.5
0
0.7 0.7 0.7
[1] 3dsi.a 0.6 0.6 0.3 0.7
0
0.1 0.1
[1] 3dsj.a 0.6 0.6 0.3 0.7 0.1
0
0.1
[1] 3dsk.a 0.6 0.7 0.3 0.7 0.1 0.1
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
2rch.a
2rcl.a
2rcm.a
3cli.a
3dsi.a
3dsj.a
3dsk.a
[1] 2rch.a
0
0.2 0.5 0.2 0.5 0.5 0.5
[1] 2rcl.a 0.2
0
0.5 0.2 0.5 0.5 0.5
[1] 2rcm.a 0.5 0.5
0
0.5 0.4 0.4 0.4
[1] 3cli.a 0.2 0.2 0.5
0
0.6 0.6 0.6
[1] 3dsi.a 0.5 0.5 0.4 0.6
0
0.2 0.2
[1] 3dsj.a 0.5 0.5 0.4 0.6 0.2
0
0.1
[1] 3dsk.a 0.5 0.5 0.4 0.6 0.2 0.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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