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BGL12_ORYSJ_24_510

Beta-glucosidase 12 [Glycosyl hydrolase 1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BGL12_ORYSJ):R: Substrate binding (473, 474)
53, 157, 158, 202, 203, 205, 206, 217, 346, 389, 417, 466, 482
53, 157, 158, 202, 203, 205, 206, 217, 346, 389, 417, 466, 473, 474, 482

Full PDB list

3ptk, 3ptm, 3ptq

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
5
3
H
1
5
7
W
1
5
8
N
2
0
2
E
2
0
3
W
2
0
5
T
2
0
6
F
2
1
7
Y
3
4
6
W
3
8
9
E
4
1
7
W
4
6
6
E
4
7
3
W
4
7
4
F
4
8
2
[1]3ptk.a none . . . . . . . . . . . . . . .
[1]3ptm.a g2f11 . . . . . . . . . . * . . . .
[1]3ptq.a nfg24 . . . . . . . . . . . . . . .

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
Q
5
3
H
1
5
7
W
1
5
8
N
2
0
2
E
2
0
3
W
2
0
5
T
2
0
6
F
2
1
7
Y
3
4
6
W
3
8
9
E
4
1
7
W
4
6
6
E
4
7
3
W
4
7
4
F
4
8
2
[1]3ptk.a . . . . . . . . . . . . . . .
[1]3ptm.a . . . . . . . . . . * . . . .
[1]3ptq.a . . . . . . . . . . . . . . .

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
3ptk.a is apo
3ptm.a:g2f
3ptq.a:nfg
[1] 3ptk.a
-
0.6 0
[1] 3ptm.a -
0.6
0
[1] 3ptq.a - 0.7
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
3ptk.a
3ptm.a
3ptq.a
[1] 3ptk.a
0
.01 .01
[1] 3ptm.a .01
0
.02
[1] 3ptq.a .01 .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
3ptk.a
3ptm.a
3ptq.a
[1] 3ptk.a
0
0.1 0.1
[1] 3ptm.a 0.1
0
0.1
[1] 3ptq.a 0.1 0.1
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

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
3ptk.a
3ptm.a
3ptq.a
[1] 3ptk.a
0
0.5 0.4
[1] 3ptm.a 0.5
0
0.4
[1] 3ptq.a 0.4 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

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