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DXR_THEMA_1_376

1-deoxy-D-xylulose 5-phosphate reductoisomerase [DXR family]

Composition of the binding site

Protein chains monomer
A1 (DXR_THEMA):163, 164, 187, 190, 192, 200, 205, 206163, 164, 187, 190, 192, 200, 205, 206
Cofactors (cF):ndp
Metals (Me):Mg

Full PDB list

3a06, 3a14

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
A
1
6
3
S
1
6
4
W
1
9
0
S
2
0
0
N
2
0
5
K
2
0
6
[1]3a06.a fom5 . . . . . . ndp Mg
[1]3a14.b none . . - . . . ndp Mg

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
A
1
6
3
S
1
6
4
H
1
8
7
W
1
9
0
M
1
9
2
S
2
0
0
N
2
0
5
K
2
0
6
[1]3a06.a . . . . . . . . ndp Mg
[1]3a14.b . . - - . . . . ndp Mg

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
3a06.a:fom
3a14.b is apo
[1] 3a06.a
0
-
[1] 3a14.b 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
3a06.a
3a14.b
[1] 3a06.a
0
0
[1] 3a14.b 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
3a06.a
3a14.b
[1] 3a06.a
0
0.7
[1] 3a14.b 0.7
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
3a06.a
3a14.b
[1] 3a06.a
0
1.0
[1] 3a14.b 1.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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