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AER_ARATH_1_345

NADPH-dependent oxidoreductase 2-alkenal reductase [NADP-dependent oxidoreductase L4BD family]

Composition of the binding site

Protein chains homodimer
A1 (AER_ARATH):53, 57, 68:70, 81, 103, 138, 260, 285:28753, 57, 68:70, 81, 103, 138, 260, 285:287
A2 (AER_ARATH):275275
Cofactors (cF):nap

Full PDB list

2j3h, 2j3i, 2j3j, 2j3k (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 A2 cF
Y
5
3
L
6
8
Q
7
0
Y
8
1
I
1
0
3
M
1
3
8
Y
2
6
0
V
2
8
5
V
2
8
6
S
2
8
7
I
2
7
5
[1]2j3i.b none . . . . . . . . . . . nap
[1]2j3j.b hc411 . . . . . . . . . . . nap
[1]2j3k.b hne11 . . . . . . . . . . . nap

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 A2 cF
Y
5
3
R
5
7
L
6
8
A
6
9
Q
7
0
Y
8
1
I
1
0
3
M
1
3
8
Y
2
6
0
V
2
8
5
V
2
8
6
S
2
8
7
I
2
7
5
[1]2j3i.b . . . . . . . . . . . . . nap
[1]2j3j.b . . . . . . . . . . . . . nap
[1]2j3k.b . . . . . . . . . . . . . nap

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
2j3i.b is apo
2j3j.b:hc4
2j3k.b:hne
[1] 2j3i.b
-
0.4 0
[1] 2j3j.b -
0
0.1
[1] 2j3k.b - 0.1
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
2j3i.b
2j3j.b
2j3k.b
[1] 2j3i.b
0
.03 .02
[1] 2j3j.b .03
0
.01
[1] 2j3k.b .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
2j3i.b
2j3j.b
2j3k.b
[1] 2j3i.b
0
0.9 0.8
[1] 2j3j.b 0.9
0
0.9
[1] 2j3k.b 0.8 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
2j3i.b
2j3j.b
2j3k.b
[1] 2j3i.b
0
1.4 1.8
[1] 2j3j.b 1.4
0
1.2
[1] 2j3k.b 1.8 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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