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BGAL_SULSO_1_489

Beta-galactosidase [Glycosyl hydrolase 1 family]

Composition of the binding site

Protein chains monomer
A1 (BGAL_SULSO):18, 150, 151, 205, 206, 209, 213, 263:265, 322, 342, 361, 387, 425, 432, 433, 44118, 150, 151, 205, 206, 209, 213, 263:265, 322, 342, 361, 387, 425, 432, 433, 441

Full PDB list

1gow, 1uwi, 1uwq, 1uwr, 1uws, 1uwt, 1uwu, 2ceq, 2cer, 4eam, 4ean, 5i3d, 5ixe (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
Q
1
8
H
1
5
0
W
1
5
1
N
2
0
5
E
2
0
6
L
2
1
3
Y
3
2
2
W
3
6
1
E
3
8
7
W
4
2
5
E
4
3
2
W
4
3
3
F
4
4
1
[1]1uwq.a none . . . . . . . . . . . . .
[1]1uwr.a gaf11 . . . . . . . . * . . . .
[1]1uws.b g2f11 . . . . . . . . * . . . .
[1]1uwt.a gtl13 . . . . . . . . . . . . .
[1]1uwu.b gox13 . . . . . . . . . . . . .
[1]2ceq.a gim14 . . . . . . . . . . . . .
[1]2cer.b pgi22 . . . . . . . . . . . . .
[1]5i3d.c none . . . . . . . . Y . . . .

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
Q
1
8
H
1
5
0
W
1
5
1
N
2
0
5
E
2
0
6
V
2
0
9
L
2
1
3
A
2
6
3
N
2
6
4
S
2
6
5
Y
3
2
2
H
3
4
2
W
3
6
1
E
3
8
7
W
4
2
5
E
4
3
2
W
4
3
3
F
4
4
1
[1]1uwq.a . . . . . . . . . . . . . . . . . .
[1]1uwr.a . . . . . . . . . . . . . * . . . .
[1]1uws.b . . . . . . . . . . . . . * . . . .
[1]1uwt.a . . . . . . . . . . . . . . . . . .
[1]1uwu.b . . . . . . . . . . . . . . . . . .
[1]2ceq.a . . . . . . . . . . . . . . . . . .
[1]2cer.b . . . . . . . . . . . . . . . . . .
[1]5i3d.c . . . . . . . . . . . . . Y . . . .

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
1uwq.a is apo
1uwr.a:gaf
1uws.b:g2f
1uwt.a:gtl
1uwu.b:gox
2ceq.a:gim
2cer.b:pgi
5i3d.c is apo
[1] 1uwq.a
-
0.4 0.6 0.4 0.6 0.8 0.6 -
[1] 1uwr.a -
0.9
1.0 0.5 0.6 1.1 0.6 -
[1] 1uws.b - 0.7
0.9
0.5 0.5 0.9 0.5 -
[1] 1uwt.a - 0.3 0.6
0.1
0.1 0.4 0.3 -
[1] 1uwu.b - 0.2 0.3 0.2
0
0.2 0.2 -
[1] 2ceq.a - 0.3 0.4 0 0
0.2
0 -
[1] 2cer.b - 0.4 0.4 0.2 0.1 0.3
0.2
-
[1] 5i3d.c - 0.9 0.8 0.7 0.9 0.9 1.3
-
[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
1uwq.a
1uwr.a
1uws.b
1uwt.a
1uwu.b
2ceq.a
2cer.b
5i3d.c
[1] 1uwq.a
0
.04 .06 .02 .04 .04 .04 .05
[1] 1uwr.a .04
0
.01 .07 .08 .08 .07 .02
[1] 1uws.b .06 .01
0
.08 .07 .07 .06 .03
[1] 1uwt.a .02 .07 .08
0
.02 .02 .03 .06
[1] 1uwu.b .04 .08 .07 .02
0
.02 .01 .08
[1] 2ceq.a .04 .08 .07 .02 .02
0
.02 .07
[1] 2cer.b .04 .07 .06 .03 .01 .02
0
.07
[1] 5i3d.c .05 .02 .03 .06 .08 .07 .07
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
1uwq.a
1uwr.a
1uws.b
1uwt.a
1uwu.b
2ceq.a
2cer.b
5i3d.c
[1] 1uwq.a
0
0.2 0.2 0.1 0.1 0.2 0.2 0.2
[1] 1uwr.a 0.2
0
0.1 0.1 0.1 0.1 0.2 0.2
[1] 1uws.b 0.2 0.1
0
0.2 0.1 0.2 0.2 0.2
[1] 1uwt.a 0.1 0.1 0.2
0
0.1 0.1 0.1 0.2
[1] 1uwu.b 0.1 0.1 0.1 0.1
0
0.1 0.1 0.2
[1] 2ceq.a 0.2 0.1 0.2 0.1 0.1
0
0.1 0.2
[1] 2cer.b 0.2 0.2 0.2 0.1 0.1 0.1
0
0.2
[1] 5i3d.c 0.2 0.2 0.2 0.2 0.2 0.2 0.2
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
1uwq.a
1uwr.a
1uws.b
1uwt.a
1uwu.b
2ceq.a
2cer.b
5i3d.c
[1] 1uwq.a
0
0.4 0.4 0.5 0.5 0.3 0.4 1.2
[1] 1uwr.a 0.4
0
0.1 0.6 0.6 0.5 0.5 1.1
[1] 1uws.b 0.4 0.1
0
0.6 0.6 0.5 0.5 1.1
[1] 1uwt.a 0.5 0.6 0.6
0
0.1 0.5 0.5 1.2
[1] 1uwu.b 0.5 0.6 0.6 0.1
0
0.5 0.5 1.2
[1] 2ceq.a 0.3 0.5 0.5 0.5 0.5
0
0.3 1.2
[1] 2cer.b 0.4 0.5 0.5 0.5 0.5 0.3
0
1.2
[1] 5i3d.c 1.2 1.1 1.1 1.2 1.2 1.2 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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