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ARAA_ECOLI_1_500

L-arabinose isomerase [Arabinose isomerase family]

Composition of the binding site

Protein chains homodimer
A1 (ARAA_ECOLI):185, 279, 306, 333, 449, 450185, 279, 306, 333, 449, 450
A2 (ARAA_ECOLI):16, 18, 19, 83, 125, 12816, 18, 19, 83, 125, 128
Metals (Me):Mn

Full PDB list

2ajt, 2hxg, 4f2d (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 A2 Me
M
1
8
5
F
2
7
9
E
3
0
6
E
3
3
3
H
4
4
9
H
4
5
0
Q
1
6
L
1
8
Y
1
9
F
8
3
Q
1
2
5
H
1
2
8
[1]2hxg.a none . . . . . . . . . . . . Mn
[1]4f2d.a rb010 * . . . . . . . . . . . Mn

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 Me
M
1
8
5
F
2
7
9
E
3
0
6
E
3
3
3
H
4
4
9
H
4
5
0
Q
1
6
L
1
8
Y
1
9
F
8
3
Q
1
2
5
H
1
2
8
[1]2hxg.a . . . . . . . . . . . . Mn
[1]4f2d.a * . . . . . . . . . . . Mn

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
2hxg.a is apo
4f2d.a:rb0
[1] 2hxg.a
-
0.2
[1] 4f2d.a -
0.3
[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
2hxg.a
4f2d.a
[1] 2hxg.a
0
.01
[1] 4f2d.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
2hxg.a
4f2d.a
[1] 2hxg.a
0
0.4
[1] 4f2d.a 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
2hxg.a
4f2d.a
[1] 2hxg.a
0
0.5
[1] 4f2d.a 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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