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BGL1_ASPAC_20_860

Beta-glucosidase 1 [Glycosyl hydrolase 3 family]

Composition of the binding site

Protein chains monomer
A1 (BGL1_ASPAC):68, 74, 92, 98, 141, 156, 189, 190, 200, 245, 248, 280, 281, 305, 451, 509, 51168, 74, 92, 98, 141, 156, 189, 190, 200, 245, 248, 280, 281, 305, 451, 509, 511
Cofactors (cF):mrd

Full PDB list

4iib, 4iic, 4iid, 4iie, 4iif, 4iig, 4iih

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
W
6
8
V
7
4
D
9
2
R
9
8
L
1
4
1
R
1
5
6
K
1
8
9
H
1
9
0
R
2
0
0
M
2
4
5
Y
2
4
8
D
2
8
0
W
2
8
1
F
3
0
5
S
4
5
1
E
5
0
9
Y
5
1
1
[1]4iib.a mrd8 . . . . . . . . . . . . . . . . .
[1]4iic.a ifm10 . . . . . . . . . . . . . . . . . mrd
[1]4iic.b ifm,mrd18 . . . . . . . . . . . . . . . . .
[1]4iid.b noj11 . . . . . . . . . . . . . . . . .
[1]4iie.a cgb,mrd20 . . . . . . . . . . . . . . . . .
[1]4iif.a cts13 . . . . . . . . . . . . . . . . .
[1]4iif.b cts,mrd21 . . . . . . . . . . . . . . . . .
[1]4iig.a none . . . . . . . . . . . . . . . . . mrd
[1]4iih.a tcb23 . . . . . . . . . . . . . . . . . mrd

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 cF
W
6
8
V
7
4
D
9
2
R
9
8
L
1
4
1
R
1
5
6
K
1
8
9
H
1
9
0
R
2
0
0
M
2
4
5
Y
2
4
8
D
2
8
0
W
2
8
1
F
3
0
5
S
4
5
1
E
5
0
9
Y
5
1
1
[1]4iib.a . . . . . . . . . . . . . . . . .
[1]4iic.a . . * . . . . . . . . . . . . . . mrd
[1]4iic.b . . * . . . . . . . . . . . . . .
[1]4iid.b . . * . . . . . . . . . . . . . .
[1]4iie.a . . * . . . . . . . . . . . . . .
[1]4iif.a . . * . . . . . . . . . . . . . .
[1]4iif.b . . * . . . . . . . . . . . . . .
[1]4iig.a . . * . . . . . . . . . . . . . . mrd
[1]4iih.a . . . . . . . . . . . . . . . . . mrd

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
4iib.a:mrd
4iic.a:ifm
4iic.b:ifm,mrd
4iid.b:noj
4iie.a:cgb,mrd
4iif.a:cts
4iif.b:cts,mrd
4iig.a is apo
4iih.a:tcb
[1] 4iib.a
0
0.2 0.3 0.2 0.8 0.4 0.3 - 0.3
[1] 4iic.a 0
0.1
0.1 0 0.6 0.1 0.1 - 1.1
[1] 4iic.b 0 0.2
0.1
0 0.4 0.1 0.3 - 1.0
[1] 4iid.b 0 0.1 0.1
0.1
0.2 0.3 0.4 - 1.2
[1] 4iie.a 0 0.1 0.2 0.2
0.6
0.3 0.3 - 0.7
[1] 4iif.a 0 0 0 0 0.3
0.1
0.1 - 0.8
[1] 4iif.b 0 0 0 0 0.3 0.1
0.1
- 1.0
[1] 4iig.a 0 0 0 0.1 0.4 0.1 0.1
-
1.0
[1] 4iih.a 0 0.2 0.2 0.1 0.7 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

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4iib.a
4iic.a
4iic.b
4iid.b
4iie.a
4iif.a
4iif.b
4iig.a
4iih.a
[1] 4iib.a
0
.09 .09 .11 .06 .08 .09 .09 .04
[1] 4iic.a .09
0
.01 .03 .04 .02 .01 .02 .06
[1] 4iic.b .09 .01
0
.02 .03 .01 0 .01 .07
[1] 4iid.b .11 .03 .02
0
.05 .03 .02 .02 .09
[1] 4iie.a .06 .04 .03 .05
0
.02 .03 .02 .05
[1] 4iif.a .08 .02 .01 .03 .02
0
.01 .02 .06
[1] 4iif.b .09 .01 0 .02 .03 .01
0
.01 .07
[1] 4iig.a .09 .02 .01 .02 .02 .02 .01
0
.08
[1] 4iih.a .04 .06 .07 .09 .05 .06 .07 .08
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
4iib.a
4iic.a
4iic.b
4iid.b
4iie.a
4iif.a
4iif.b
4iig.a
4iih.a
[1] 4iib.a
0
0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.1
[1] 4iic.a 0.1
0
0.1 0.2 0.1 0.2 0.2 0.1 0.1
[1] 4iic.b 0.1 0.1
0
0.1 0.1 0.1 0.1 0.1 0.1
[1] 4iid.b 0.2 0.2 0.1
0
0.1 0.1 0.1 0.2 0.2
[1] 4iie.a 0.2 0.1 0.1 0.1
0
0.1 0.2 0.1 0.1
[1] 4iif.a 0.2 0.2 0.1 0.1 0.1
0
0.2 0.1 0.2
[1] 4iif.b 0.2 0.2 0.1 0.1 0.2 0.2
0
0.2 0.2
[1] 4iig.a 0.2 0.1 0.1 0.2 0.1 0.1 0.2
0
0.2
[1] 4iih.a 0.1 0.1 0.1 0.2 0.1 0.2 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
4iib.a
4iic.a
4iic.b
4iid.b
4iie.a
4iif.a
4iif.b
4iig.a
4iih.a
[1] 4iib.a
0
0.4 0.5 0.5 0.3 0.5 0.5 0.4 0.1
[1] 4iic.a 0.4
0
0.3 0.3 0.3 0.5 0.3 0.4 0.3
[1] 4iic.b 0.5 0.3
0
0.2 0.4 0.4 0.2 0.3 0.4
[1] 4iid.b 0.5 0.3 0.2
0
0.4 0.4 0.2 0.3 0.5
[1] 4iie.a 0.3 0.3 0.4 0.4
0
0.4 0.4 0.3 0.2
[1] 4iif.a 0.5 0.5 0.4 0.4 0.4
0
0.4 0.3 0.5
[1] 4iif.b 0.5 0.3 0.2 0.2 0.4 0.4
0
0.4 0.5
[1] 4iig.a 0.4 0.4 0.3 0.3 0.3 0.3 0.4
0
0.4
[1] 4iih.a 0.1 0.3 0.4 0.5 0.2 0.5 0.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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