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C74A2_PARAR_1_473

Allene oxide synthase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (C74A2_PARAR):R: Substrate binding (275)
R: Substrate binding (344, 346)
199, 202, 206, 212, 279, 282, 459
199, 202, 206, 212, 275, 279, 282, 344, 346, 459
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3dam, 3dan, 3dbm (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
S
1
9
9
V
2
0
2
L
2
0
6
L
2
1
2
F
2
7
5
G
2
7
9
K
2
8
2
V
3
4
4
P
3
4
6
[1]3dan.a none . . . . . . . . . hem Fe
[1]3dbm.a ho221 . . . . . . . . . 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
S
1
9
9
V
2
0
2
L
2
0
6
L
2
1
2
F
2
7
5
G
2
7
9
K
2
8
2
V
3
4
4
P
3
4
6
L
4
5
9
[1]3dan.a . . . . . . . . . * hem Fe
[1]3dbm.a . . . . . . . . . . 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
3dan.a is apo
3dbm.a:ho2
[1] 3dan.a
-
1.1
[1] 3dbm.a -
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
3dan.a
3dbm.a
[1] 3dan.a
0
.11
[1] 3dbm.a .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
3dan.a
3dbm.a
[1] 3dan.a
0
0.6
[1] 3dbm.a 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
3dan.a
3dbm.a
[1] 3dan.a
0
1.4
[1] 3dbm.a 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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