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ALSE_ECOLI_1_231

D-allulose-6-phosphate 3-epimerase [Ribulose-phosphate 3-epimerase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ALSE_ECOLI):R: Substrate binding (140:143)
R: Substrate binding (173:175)
R: Substrate binding (195:197)
6, 8, 9, 30, 32, 63, 65, 135, 139
6, 8, 9, 30, 32, 63, 65, 135, 139:143, 173:175, 195:197
Metals (Me):Mg

Full PDB list

3ct7, 3ctl

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
S
6
M
8
C
9
H
3
0
D
3
2
H
6
3
M
6
5
M
1
3
5
P
1
3
9
G
1
4
0
F
1
4
1
A
1
4
2
G
1
4
3
D
1
7
3
G
1
7
4
S
1
7
5
G
1
9
5
T
1
9
6
S
1
9
7
[1]3ct7.a none . . . . . . . . . . . . . . . . . . . Mg
[1]3ctl.a s6p16 . . . . . . . . . . . . . . . . . . . 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

[download in TSV format]
   
PDB.ch
A1 Me
S
6
M
8
C
9
H
3
0
D
3
2
H
6
3
M
6
5
M
1
3
5
P
1
3
9
G
1
4
0
F
1
4
1
A
1
4
2
G
1
4
3
D
1
7
3
G
1
7
4
S
1
7
5
G
1
9
5
T
1
9
6
S
1
9
7
[1]3ct7.a . . . . . . . . . . . . . . . . . . . Mg
[1]3ctl.a . . . . . . . . . . . . . . . . . . . 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
3ct7.a is apo
3ctl.a:s6p
[1] 3ct7.a
-
0
[1] 3ctl.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
3ct7.a
3ctl.a
[1] 3ct7.a
0
0
[1] 3ctl.a 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 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
3ct7.a
3ctl.a
[1] 3ct7.a
0
0.2
[1] 3ctl.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
3ct7.a
3ctl.a
[1] 3ct7.a
0
0.2
[1] 3ctl.a 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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