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BGAL_HUMAN_22_677

Beta-galactosidase [Glycosyl hydrolase 35 family]

Composition of the binding site

Protein chains monomer
A1 (BGAL_HUMAN):83, 126:129, 187, 188, 227, 241, 268, 270, 273, 274, 276, 306, 321, 333, 48583, 126:129, 187, 188, 227, 241, 268, 270, 273, 274, 276, 306, 321, 333, 485

Full PDB list

3thc, 3thd, 3wez, 3wf0, 3wf1, 3wf2, 3wf3, 3wf4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
8
3
I
1
2
6
C
1
2
7
A
1
2
8
E
1
2
9
N
1
8
7
E
1
8
8
E
2
6
8
Y
2
7
0
W
2
7
3
L
2
7
4
H
2
7
6
Y
3
0
6
N
3
2
1
Y
3
3
3
Y
4
8
5
[1]3thd.a dgj11 . . . . . . . . . . . . . . . .
[1]3wez.b n8v20 . . . . . . . . . . . . . . . .
[1]3wf0.a 6dj17 . . . . . . . . . . . . . . . .
[1]3wf1.a 6gj18 . . . . . . . . . . . . . . . .
[1]3wf2.a ndj18 . . . . . . . . . . . . . . . .
[1]3wf3.c none . . . . . . . . . . . . . . . .

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
Y
8
3
I
1
2
6
C
1
2
7
A
1
2
8
E
1
2
9
N
1
8
7
E
1
8
8
F
2
2
7
D
2
4
1
E
2
6
8
Y
2
7
0
W
2
7
3
L
2
7
4
H
2
7
6
Y
3
0
6
N
3
2
1
Y
3
3
3
Y
4
8
5
[1]3thd.a . . . . . . . . . . . . . . . . . .
[1]3wez.b . . . . . . . . . . . . . . . . . .
[1]3wf0.a . . . . . . . . . . . . . . . . * .
[1]3wf1.a . . . . . . . . . . . . . . . . . .
[1]3wf2.a . . . . . . . . . . . . . . . . . .
[1]3wf3.c . . . . . . . . . . . . . . . . . .

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
3thd.a:dgj
3wez.b:n8v
3wf0.a:6dj
3wf1.a:6gj
3wf2.a:ndj
3wf3.c is apo
[1] 3thd.a
0
0.2 0.1 0.3 0 -
[1] 3wez.b 0
0
0.1 0.4 0 -
[1] 3wf0.a 0.4 0.8
0
0.3 0.3 -
[1] 3wf1.a 0.1 0.3 0.1
0.2
0.2 -
[1] 3wf2.a 0 0.1 0.1 0.2
0
-
[1] 3wf3.c 0 0.1 0 0.3 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
3thd.a
3wez.b
3wf0.a
3wf1.a
3wf2.a
3wf3.c
[1] 3thd.a
0
.02 .04 .01 .03 .01
[1] 3wez.b .02
0
.06 .03 .03 .02
[1] 3wf0.a .04 .06
0
.04 .04 .04
[1] 3wf1.a .01 .03 .04
0
.03 .02
[1] 3wf2.a .03 .03 .04 .03
0
.02
[1] 3wf3.c .01 .02 .04 .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
3thd.a
3wez.b
3wf0.a
3wf1.a
3wf2.a
3wf3.c
[1] 3thd.a
0
0.1 0.1 0.2 0.2 0.1
[1] 3wez.b 0.1
0
0.1 0.2 0.2 0.1
[1] 3wf0.a 0.1 0.1
0
0.2 0.2 0.2
[1] 3wf1.a 0.2 0.2 0.2
0
0.2 0.2
[1] 3wf2.a 0.2 0.2 0.2 0.2
0
0.2
[1] 3wf3.c 0.1 0.1 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
3thd.a
3wez.b
3wf0.a
3wf1.a
3wf2.a
3wf3.c
[1] 3thd.a
0
0.4 0.5 0.4 0.6 0.4
[1] 3wez.b 0.4
0
0.3 0.2 0.4 0.2
[1] 3wf0.a 0.5 0.3
0
0.3 0.5 0.3
[1] 3wf1.a 0.4 0.2 0.3
0
0.4 0.3
[1] 3wf2.a 0.6 0.4 0.5 0.4
0
0.4
[1] 3wf3.c 0.4 0.2 0.3 0.3 0.4
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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