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EBDG_AMYOR_1_906

Exo-beta-D-glucosaminidase [Glycosyl hydrolase 2 family]

Composition of the binding site

Protein chains monomer
A1 (EBDG_AMYOR):202:204, 394, 419, 420, 431, 468, 469, 512, 513, 516, 541, 583, 642, 653, 781202:204, 394, 419, 420, 431, 468, 469, 512, 513, 516, 541, 583, 642, 653, 781
Metals (Me):Cd

Full PDB list

2vzo, 2vzs, 2vzt, 2vzu, 2vzv, 2x05, 2x09

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
2
0
2
D
2
0
3
W
2
0
4
E
3
9
4
C
4
1
9
C
4
2
0
E
4
3
1
D
4
6
9
M
5
1
2
Y
5
1
6
E
5
4
1
F
5
8
3
W
6
4
2
W
6
5
3
W
7
8
1
[1]2vzo.a cd1 . . . . . . . E . . . . . . .
[1]2vzs.a gcs12 . . . . . . . . . . . . . . . Cd
[1]2vzt.a pnj21 . . . . . . . . . . A . . . . Cd
[1]2vzu.a pnj21 . . . . . . . A . . . . . . . Cd
[1]2vzv.a gcs.gcs23 . . . . . . . . . . A . . . .
[1]2x05.b x0513 . . . . . . . . . . . . . . . Cd
[1]2x09.b x0913 . . . . . . . . . . . . . . . Cd

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
I
2
0
2
D
2
0
3
W
2
0
4
E
3
9
4
C
4
1
9
C
4
2
0
E
4
3
1
S
4
6
8
D
4
6
9
M
5
1
2
N
5
1
3
Y
5
1
6
E
5
4
1
F
5
8
3
W
6
4
2
W
6
5
3
W
7
8
1
[1]2vzo.a . . . . . . . . E . . . . . . . .
[1]2vzs.a . . . . . . . . . . . . . . . . . Cd
[1]2vzt.a . . . . . . . . . . . . A . . . . Cd
[1]2vzu.a . . . . . . . . A . . . . . . . . Cd
[1]2vzv.a . . . . . . . . . . . . A . . . .
[1]2x05.b . . . . . . . . . . . . . . . . . Cd
[1]2x09.b . . . . . . . . . . . . . . . . . Cd

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
2vzo.a:cd
2vzs.a:gcs
2vzt.a:pnj
2vzu.a:pnj
2vzv.a:gcs.gcs
2x05.b:x05
2x09.b:x09
[1] 2vzo.a
0.1
0.1 0.4 0.5 0.2 0.4 0.7
[1] 2vzs.a 0.2
0
0.4 0.4 0.2 0.4 0.4
[1] 2vzt.a 0 0.1
0.1
0.1 0.1 0.3 0.5
[1] 2vzu.a 0.1 0 0.5
0.1
0.2 0.4 0.4
[1] 2vzv.a 0.2 0.2 0.3 0.6
0
0.3 0.6
[1] 2x05.b 0.1 0.2 0.4 0.4 0.2
0.2
0.3
[1] 2x09.b 0.1 0.1 0.5 0.4 0.2 0.2
0.3
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
2vzo.a
2vzs.a
2vzt.a
2vzu.a
2vzv.a
2x05.b
2x09.b
[1] 2vzo.a
0
.04 .06 .05 .04 .03 .03
[1] 2vzs.a .04
0
.07 .03 .04 .02 .02
[1] 2vzt.a .06 .07
0
.04 .05 .06 .06
[1] 2vzu.a .05 .03 .04
0
.06 .04 .04
[1] 2vzv.a .04 .04 .05 .06
0
.04 .04
[1] 2x05.b .03 .02 .06 .04 .04
0
0
[1] 2x09.b .03 .02 .06 .04 .04 0
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

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
2vzo.a
2vzs.a
2vzt.a
2vzu.a
2vzv.a
2x05.b
2x09.b
[1] 2vzo.a
0
0.4 0.5 0.4 0.5 0.5 0.5
[1] 2vzs.a 0.4
0
0.2 0.1 0.2 0.3 0.3
[1] 2vzt.a 0.5 0.2
0
0.2 0.3 0.3 0.3
[1] 2vzu.a 0.4 0.1 0.2
0
0.3 0.3 0.3
[1] 2vzv.a 0.5 0.2 0.3 0.3
0
0.3 0.3
[1] 2x05.b 0.5 0.3 0.3 0.3 0.3
0
0.1
[1] 2x09.b 0.5 0.3 0.3 0.3 0.3 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2vzo.a
2vzs.a
2vzt.a
2vzu.a
2vzv.a
2x05.b
2x09.b
[1] 2vzo.a
0
0.5 0.4 0.4 0.5 0.5 0.5
[1] 2vzs.a 0.5
0
0.6 0.1 0.3 0.5 0.5
[1] 2vzt.a 0.4 0.6
0
0.3 0.6 0.7 0.7
[1] 2vzu.a 0.4 0.1 0.3
0
0.3 0.5 0.4
[1] 2vzv.a 0.5 0.3 0.6 0.3
0
0.5 0.5
[1] 2x05.b 0.5 0.5 0.7 0.5 0.5
0
0.3
[1] 2x09.b 0.5 0.5 0.7 0.4 0.5 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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