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DBR2_ARTAN_1_387

Artemisinic aldehyde Delta(11(13)) reductase [NADH:flavin oxidoreductase/NADH oxidase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DBR2_ARTAN):R: Substrate-binding (180, 183)
25:28, 59, 101, 232, 275, 316:318, 338:340, 366, 367
25:28, 59, 101, 180, 183, 232, 275, 316:318, 338:340, 366, 367

Full PDB list

5dxx, 5dxy, 5dy2, 5dy3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
2
5
P
2
6
M
2
7
T
2
8
G
5
9
Q
1
0
1
H
1
8
0
H
1
8
3
R
2
3
2
T
2
7
5
C
3
1
6
G
3
1
7
G
3
1
8
F
3
3
8
G
3
3
9
R
3
4
0
F
3
6
6
Y
3
6
7
[1]5dxx.a fmn31 . . . . . . . . . . . . . . . . . .
[1]5dy2.a fmn31 . . L . . . . . . . . . . . . . . .

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
A
2
5
P
2
6
M
2
7
T
2
8
G
5
9
Q
1
0
1
H
1
8
0
H
1
8
3
R
2
3
2
T
2
7
5
C
3
1
6
G
3
1
7
G
3
1
8
F
3
3
8
G
3
3
9
R
3
4
0
F
3
6
6
Y
3
6
7
[1]5dxx.a . . . . . . . . . . . . . . . . . .
[1]5dy2.a . . L . . . . . . . . . . . . . . .

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
5dxx.a:fmn
5dy2.a:fmn
[1] 5dxx.a
0.1
0.3
[1] 5dy2.a 0
0.1
[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
5dxx.a
5dy2.a
[1] 5dxx.a
0
.01
[1] 5dy2.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
5dxx.a
5dy2.a
[1] 5dxx.a
0
0.2
[1] 5dy2.a 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
5dxx.a
5dy2.a
[1] 5dxx.a
0
0.3
[1] 5dy2.a 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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