If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

BGLR_ECOLI_1_603

Beta-glucuronidase [Glycosyl hydrolase 2 family]

Composition of the binding site

Protein chains monomer
A1 (BGLR_ECOLI):160:163, 360:364, 413, 446:448, 468, 469, 471:473, 504, 556, 557, 559:562160:163, 360:364, 413, 446:448, 468, 469, 471:473, 504, 556, 557, 559:562

Full PDB list

3k46, 3k4a, 3k4d, 3lpf, 3lpg, 4jhz, 5czk (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
1
6
2
D
1
6
3
L
3
6
1
G
3
6
2
I
3
6
3
E
4
1
3
V
4
4
6
M
4
4
7
F
4
4
8
Y
4
6
8
Y
4
6
9
W
4
7
1
Y
4
7
2
V
4
7
3
S
5
5
7
L
5
6
1
R
5
6
2
[1]3k4a.a none . . . . . . . * . . . . . . . . .
[1]3k4d.b none . . . . - . . . . . . . . . . . .
[1]3lpf.a z7729 . . . . . . . * . . . . . . . . .
[1]3lpg.a z7827 . . . . . . . * . . . . . . . . .
[1]4jhz.a 1kv30 . . . - - . . * . . . . . . . . .
[2]5czk.b 57z28 . . . . . . . * . . . . . . . . .

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
Y
1
6
0
F
1
6
1
H
1
6
2
D
1
6
3
S
3
6
0
L
3
6
1
G
3
6
2
I
3
6
3
G
3
6
4
E
4
1
3
V
4
4
6
M
4
4
7
F
4
4
8
Y
4
6
8
Y
4
6
9
W
4
7
1
Y
4
7
2
V
4
7
3
E
5
0
4
T
5
5
6
S
5
5
7
G
5
5
9
I
5
6
0
L
5
6
1
R
5
6
2
[1]3k4a.a . . . . . . . . - . . * . . . . . . . . . . . . .
[1]3k4d.b . . . . . * . - - . . . . . . . . . . . . . . . .
[1]3lpf.a . . . . . . . . . . . * . . . . . . . . . . . . .
[1]3lpg.a . . . . . . . . . . . * . . . . . . . . . . . . .
[1]4jhz.a . . . . . . - - - . . * . . . . . . . . . . . . .
[2]5czk.b . . . . . * . * . . . * . . . . . . . . . . * . .

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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3k4a.a is apo
3k4d.b is apo
3lpf.a:z77
3lpg.a:z78
4jhz.a:1kv
5czk.b:57z
[1] 3k4a.a
-
- 0.7 0.8 0.5 1.6
[1] 3k4d.b -
-
1.0 1.5 0.4 0.9
[1] 3lpf.a - -
0
0 0.3 0.9
[1] 3lpg.a - - 0.1
0.2
0.4 1.0
[1] 4jhz.a - - 0.6 0.6
0
1.7
[2] 5czk.b - - 4.7 4.9 3.4
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3k4a.a
3k4d.b
3lpf.a
3lpg.a
4jhz.a
5czk.b
[1] 3k4a.a
0
.07 .04 .03 .05 .24
[1] 3k4d.b .07
0
.06 .06 .06 .29
[1] 3lpf.a .04 .06
0
.02 .03 .26
[1] 3lpg.a .03 .06 .02
0
.02 .25
[1] 4jhz.a .05 .06 .03 .02
0
.25
[2] 5czk.b .24 .29 .26 .25 .25
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
3k4a.a
3k4d.b
3lpf.a
3lpg.a
4jhz.a
5czk.b
[1] 3k4a.a
0
1.5 1.7 1.6 1.5 2.3
[1] 3k4d.b 1.5
0
0.7 0.7 0.8 2.5
[1] 3lpf.a 1.7 0.7
0
0.5 0.6 2.6
[1] 3lpg.a 1.6 0.7 0.5
0
0.6 2.6
[1] 4jhz.a 1.5 0.8 0.6 0.6
0
2.6
[2] 5czk.b 2.3 2.5 2.6 2.6 2.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
3k4a.a
3k4d.b
3lpf.a
3lpg.a
4jhz.a
5czk.b
[1] 3k4a.a
0
1.9 2.0 1.9 1.8 4.2
[1] 3k4d.b 1.9
0
0.7 0.7 1.1 4.5
[1] 3lpf.a 2.0 0.7
0
0.4 1.0 4.4
[1] 3lpg.a 1.9 0.7 0.4
0
1.0 4.4
[1] 4jhz.a 1.8 1.1 1.0 1.0
0
4.5
[2] 5czk.b 4.2 4.5 4.4 4.4 4.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...