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BGL07_ORYSJ_25_504

Beta-glucosidase 7 [Glycosyl hydrolase 1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BGL07_ORYSJ):R: Substrate binding (468, 469)
57, 158, 159, 203, 204, 206, 207, 210, 211, 215, 271, 273, 275, 341, 343, 346, 348, 365, 369, 371, 386, 414, 461, 477
57, 158, 159, 203, 204, 206, 207, 210, 211, 215, 271, 273, 275, 341, 343, 346, 348, 365, 369, 371, 386, 414, 461, 468, 469, 477

Full PDB list

2rgl, 2rgm, 3aht, 3ahv, 3f4v, 3f5j, 3f5k, 3f5l, 3scn, 3sco, 3scp, 3scq, 3scr, 3scs, 3sct, 3scu, 3scv, 3scw, 4qlj, 4qlk, 4qll (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Q
5
7
H
1
5
8
Y
1
5
9
N
2
0
3
E
2
0
4
R
2
0
6
I
2
0
7
L
2
1
0
L
2
1
1
Q
2
1
5
D
2
7
1
N
2
7
3
Y
2
7
5
N
3
4
1
Y
3
4
3
M
3
4
8
W
3
6
5
Y
3
6
9
F
3
7
1
W
3
8
6
E
4
1
4
W
4
6
1
E
4
6
8
W
4
6
9
F
4
7
7
[1]2rgl.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2rgm.a g2f11 . . . . . . . . . . . . . . . . . . . . * . . . .
[1]3ahv.a g2f11 . . . . Q . . . . . . . . . . . . . . . * . . . .
[1]3f4v.a none . . . . Q . . . . . . . . . . . . . . . . . . . .
[1]3f5j.a ctt45 . . . . Q . . . . . . . . . . . . . . . . . . . .
[1]3f5k.a ce556 . . . . Q . . . . . . . . . . . . . . . . . . . .
[1]3f5l.a lb223 . . . . Q . . . . . . . . . . . . . . . . . . . .
[1]3scn.a none . . . . . . . . . . . . . . . . . . . . G . . . .
[1]3sco.a glf12 . . . . . . . . . . . . . . . . . . . . G . . . .
[1]3scp.a none . . . . . . . . . . . . . . . . . . . . A . . . .
[1]3scq.a glf12 . . . . . . . . . . . . . . . . . . . . A . . . .
[1]3scr.a none . . . . . . . . . . . . . . . . . . . . S . . . .
[1]3scs.a glf12 . . . . . . . . . . . . . . . . . . . . S . . . .
[1]3sct.a ctt45 . . . . . . . . . . . . . . . . . . . . G . . . .
[1]3scu.a ce556 . . . . . . . . . . . . . . . . . . . . G . . . .
[1]3scw.a ctt45 . . . . . . . . . . . . . . . . . A . . G . . . .
[1]4qlj.a ctt45 . . . . . . . . . A . . . . . . . A . . G . . . .
[1]4qlk.a ctt45 . . . . Q . . . . . . . . . . . . A . . . . . . .
[1]4qll.a ctt45 . . . . Q . . . . A . . . . . . . A . . . . . . .

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
7
H
1
5
8
Y
1
5
9
N
2
0
3
E
2
0
4
R
2
0
6
I
2
0
7
L
2
1
0
L
2
1
1
Q
2
1
5
D
2
7
1
N
2
7
3
Y
2
7
5
N
3
4
1
Y
3
4
3
S
3
4
6
M
3
4
8
W
3
6
5
Y
3
6
9
F
3
7
1
W
3
8
6
E
4
1
4
W
4
6
1
E
4
6
8
W
4
6
9
F
4
7
7
[1]2rgl.a . . . . . . . . . * . . . . . . . . * . . * . . . .
[1]2rgm.a . . . . . . . . . * . . . . . . . . * . . * . . . .
[1]3ahv.a . . . . Q . . . . * . . . . . . . . * . . * . . . .
[1]3f4v.a . . . . Q . . . . * . . . . . . . . . . . * . . . .
[1]3f5j.a . . . . Q . . . . * . . . . . . . . * . . * . . . .
[1]3f5k.a . . . . Q . . . . * . . . . . . . . * . . * . . . .
[1]3f5l.a . . . . Q . . . . * . . . . . . . . . . . * . . . .
[1]3scn.a . . . . . . . . . * . . . . . . . . * . . G . . . .
[1]3sco.a . . . . . . . . . * . . . . . . . . * . . G . . . .
[1]3scp.a . . . . . . . . . * . . . . . . . . * . . A . . . .
[1]3scq.a . . . . . . . . . * . . . . . . . . * . . A . . . .
[1]3scr.a . . . . . . . . . * . . . . . . . . * . . S . . . .
[1]3scs.a . . . . . . . . . * . . . . . . . . * . . S . . . .
[1]3sct.a . . . . . . . . . * . . . . . . . . * . . G . . . .
[1]3scu.a . . . . . . . . . * . . . . . . . . * . . G . . . .
[1]3scw.a . . . . . . . . . . . . . . . . . . A . . G . . . .
[1]4qlj.a . . . . . . . . . A . . . . . . . . A . . G . . . .
[1]4qlk.a . . . . Q . . . . * . . . . . . . . A . . * . . . .
[1]4qll.a . . . . Q . . . . A . . . . . . . . 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
2rgl.a is apo
2rgm.a:g2f
3ahv.a:g2f
3f4v.a is apo
3f5j.a:ctt
3f5k.a:ce5
3f5l.a:lb2
3scn.a is apo
3sco.a:glf
3scp.a is apo
3scq.a:glf
3scr.a is apo
3scs.a:glf
3sct.a:ctt
3scu.a:ce5
3scw.a:ctt
4qlj.a:ctt
4qlk.a:ctt
4qll.a:ctt
[1] 2rgl.a
-
0.6 0.6 - 0.2 0.4 0.3 - 1.1 - 1.1 - 1.2 0.2 0.6 1.2 1.8 3.4 3.4
[1] 2rgm.a -
0.9
0.7 - 0.1 0.1 0.2 - 1.6 - 1.4 - 1.4 0.2 0.4 1.5 1.8 3.2 2.8
[1] 3ahv.a - 0.9
0.9
- 0.1 0.1 0.4 - 1.6 - 1.6 - 1.6 0.2 0.4 1.6 2.2 2.4 2.5
[1] 3f4v.a - 0.6 0.6
-
0.4 0.4 0.4 - 1.1 - 1.1 - 1.3 0.5 0.7 1.3 1.8 0.4 0.3
[1] 3f5j.a - 0.5 0.5 -
0.2
0.3 0.4 - 1.1 - 1.1 - 1.2 0.3 0.4 1.4 1.7 2.8 2.8
[1] 3f5k.a - 0.6 0.6 - 0.2
0.2
0.4 - 1.2 - 1.1 - 1.2 0.4 0.4 1.4 1.7 2.8 2.8
[1] 3f5l.a - 0.5 0.3 - 0.2 0.3
0.4
- 1.1 - 1.1 - 1.3 0.4 0.5 1.0 1.7 0.2 0.2
[1] 3scn.a - 0.2 0.3 - 0.2 0.2 0.5
-
0.2 - 0.2 - 0.2 0.1 0.2 1.4 2.0 2.9 2.7
[1] 3sco.a - 0.2 0.2 - 0.1 0.1 0 -
0
- 0 - 0 0.1 0 1.1 1.6 2.9 2.7
[1] 3scp.a - 0.2 0.2 - 0.3 0.1 0.5 - 0.2
-
0.2 - 0.2 0.1 0.2 1.4 1.7 2.9 2.9
[1] 3scq.a - 0.2 0.2 - 0.1 0.1 0.1 - 0 -
0
- 0 0.1 0.2 1.1 1.4 3.1 2.9
[1] 3scr.a - 0.2 0.2 - 0.2 0.2 0.6 - 0.2 - 0.2
-
0.2 0.1 0.3 1.1 1.6 2.8 2.8
[1] 3scs.a - 0.2 0.2 - 0.1 0.1 0 - 0 - 0 -
0
0 0 1.0 1.4 2.7 2.7
[1] 3sct.a - 0.3 0.3 - 0.3 0.3 0.4 - 0.1 - 0.1 - 0.1
0.1
0.2 0.8 1.6 2.9 2.9
[1] 3scu.a - 0.3 0.3 - 0.3 0.3 0.3 - 0.3 - 0.3 - 0.2 0.2
0.1
0.8 1.7 2.9 2.9
[1] 3scw.a - 0.3 0.3 - 0.1 0.2 0.2 - 0.1 - 0.1 - 0.1 0.1 0.2
0.2
0.8 0.2 0.2
[1] 4qlj.a - 0.3 0.3 - 0.1 0.2 0.1 - 0.1 - 0.1 - 0.1 0.1 0.2 0.1
0.2
0.2 0.2
[1] 4qlk.a - 0.6 0.5 - 0.1 0.2 0.3 - 1.2 - 1.2 - 1.2 0.3 0.4 0.9 1.7
0.2
0.2
[1] 4qll.a - 0.7 0.6 - 0.2 0.3 0.4 - 1.2 - 1.2 - 1.2 0.3 0.4 0.3 0.4 0.2
0.2
[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
2rgl.a
2rgm.a
3ahv.a
3f4v.a
3f5j.a
3f5k.a
3f5l.a
3scn.a
3sco.a
3scp.a
3scq.a
3scr.a
3scs.a
3sct.a
3scu.a
3scw.a
4qlj.a
4qlk.a
4qll.a
[1] 2rgl.a
0
.04 .08 .13 .03 .03 .13 .10 .08 .08 .06 .08 .08 .08 .08 .21 .23 .13 .18
[1] 2rgm.a .04
0
.05 .15 .05 .05 .15 .11 .09 .10 .08 .09 .09 .10 .10 .22 .24 .15 .20
[1] 3ahv.a .08 .05
0
.14 .05 .05 .13 .10 .10 .09 .12 .09 .10 .10 .09 .22 .23 .13 .18
[1] 3f4v.a .13 .15 .14
0
.11 .11 .01 .17 .18 .16 .18 .15 .17 .16 .16 .09 .11 .01 .06
[1] 3f5j.a .03 .05 .05 .11
0
0 .10 .07 .08 .05 .08 .05 .06 .05 .05 .18 .20 .10 .15
[1] 3f5k.a .03 .05 .05 .11 0
0
.10 .06 .07 .06 .07 .05 .05 .05 .05 .18 .20 .10 .15
[1] 3f5l.a .13 .15 .13 .01 .10 .10
0
.17 .18 .15 .18 .15 .16 .15 .15 .08 .10 0 .05
[1] 3scn.a .10 .11 .10 .17 .07 .06 .17
0
.03 .01 .05 .02 .03 .02 .01 .15 .18 .17 .21
[1] 3sco.a .08 .09 .10 .18 .08 .07 .18 .03
0
.04 .02 .04 .02 .03 .03 .15 .17 .18 .22
[1] 3scp.a .08 .10 .09 .16 .05 .06 .15 .01 .04
0
.05 .01 .03 .02 .01 .15 .17 .15 .21
[1] 3scq.a .06 .08 .12 .18 .08 .07 .18 .05 .02 .05
0
.04 .02 .03 .04 .15 .17 .18 .22
[1] 3scr.a .08 .09 .09 .15 .05 .05 .15 .02 .04 .01 .04
0
.02 .02 .02 .15 .17 .15 .20
[1] 3scs.a .08 .09 .10 .17 .06 .05 .16 .03 .02 .03 .02 .02
0
.01 .02 .13 .15 .16 .20
[1] 3sct.a .08 .10 .10 .16 .05 .05 .15 .02 .03 .02 .03 .02 .01
0
.01 .13 .16 .15 .20
[1] 3scu.a .08 .10 .09 .16 .05 .05 .15 .01 .03 .01 .04 .02 .02 .01
0
.14 .17 .15 .20
[1] 3scw.a .21 .22 .22 .09 .18 .18 .08 .15 .15 .15 .15 .15 .13 .13 .14
0
.03 .08 .08
[1] 4qlj.a .23 .24 .23 .11 .20 .20 .10 .18 .17 .17 .17 .17 .15 .16 .17 .03
0
.10 .05
[1] 4qlk.a .13 .15 .13 .01 .10 .10 0 .17 .18 .15 .18 .15 .16 .15 .15 .08 .10
0
.05
[1] 4qll.a .18 .20 .18 .06 .15 .15 .05 .21 .22 .21 .22 .20 .20 .20 .20 .08 .05 .05
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
2rgl.a
2rgm.a
3ahv.a
3f4v.a
3f5j.a
3f5k.a
3f5l.a
3scn.a
3sco.a
3scp.a
3scq.a
3scr.a
3scs.a
3sct.a
3scu.a
3scw.a
4qlj.a
4qlk.a
4qll.a
[1] 2rgl.a
0
0.2 0.2 0.3 0.2 0.2 0.3 0.2 0.1 0.2 0.1 0.2 0.1 0.2 0.2 0.3 0.3 0.3 0.3
[1] 2rgm.a 0.2
0
0.2 0.4 0.2 0.2 0.4 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3
[1] 3ahv.a 0.2 0.2
0
0.3 0.1 0.1 0.3 0.2 0.2 0.1 0.2 0.1 0.2 0.1 0.2 0.2 0.2 0.3 0.2
[1] 3f4v.a 0.3 0.4 0.3
0
0.3 0.3 0.1 0.3 0.2 0.3 0.3 0.3 0.2 0.3 0.3 0.4 0.4 0.4 0.4
[1] 3f5j.a 0.2 0.2 0.1 0.3
0
0.1 0.3 0.2 0.2 0.1 0.2 0.1 0.2 0.1 0.1 0.2 0.2 0.2 0.2
[1] 3f5k.a 0.2 0.2 0.1 0.3 0.1
0
0.3 0.2 0.2 0.1 0.2 0.1 0.2 0.1 0.1 0.2 0.2 0.2 0.2
[1] 3f5l.a 0.3 0.4 0.3 0.1 0.3 0.3
0
0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.3 0.4 0.4 0.4 0.4
[1] 3scn.a 0.2 0.3 0.2 0.3 0.2 0.2 0.3
0
0.2 0.1 0.2 0.1 0.2 0.1 0.1 0.2 0.2 0.3 0.3
[1] 3sco.a 0.1 0.2 0.2 0.2 0.2 0.2 0.3 0.2
0
0.1 0.1 0.1 0.1 0.2 0.2 0.3 0.3 0.3 0.3
[1] 3scp.a 0.2 0.2 0.1 0.3 0.1 0.1 0.3 0.1 0.1
0
0.2 0.1 0.2 0.1 0.1 0.2 0.2 0.2 0.2
[1] 3scq.a 0.1 0.2 0.2 0.3 0.2 0.2 0.3 0.2 0.1 0.2
0
0.1 0.1 0.2 0.2 0.3 0.3 0.3 0.3
[1] 3scr.a 0.2 0.2 0.1 0.3 0.1 0.1 0.3 0.1 0.1 0.1 0.1
0
0.2 0.1 0.1 0.2 0.2 0.3 0.2
[1] 3scs.a 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.1 0.2 0.1 0.2
0
0.2 0.2 0.3 0.3 0.3 0.3
[1] 3sct.a 0.2 0.2 0.1 0.3 0.1 0.1 0.3 0.1 0.2 0.1 0.2 0.1 0.2
0
0.1 0.2 0.2 0.2 0.2
[1] 3scu.a 0.2 0.3 0.2 0.3 0.1 0.1 0.3 0.1 0.2 0.1 0.2 0.1 0.2 0.1
0
0.2 0.2 0.3 0.2
[1] 3scw.a 0.3 0.3 0.2 0.4 0.2 0.2 0.4 0.2 0.3 0.2 0.3 0.2 0.3 0.2 0.2
0
0.1 0.1 0.1
[1] 4qlj.a 0.3 0.3 0.2 0.4 0.2 0.2 0.4 0.2 0.3 0.2 0.3 0.2 0.3 0.2 0.2 0.1
0
0.1 0.1
[1] 4qlk.a 0.3 0.3 0.3 0.4 0.2 0.2 0.4 0.3 0.3 0.2 0.3 0.3 0.3 0.2 0.3 0.1 0.1
0
0.1
[1] 4qll.a 0.3 0.3 0.2 0.4 0.2 0.2 0.4 0.3 0.3 0.2 0.3 0.2 0.3 0.2 0.2 0.1 0.1 0.1
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

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
2rgl.a
2rgm.a
3ahv.a
3f4v.a
3f5j.a
3f5k.a
3f5l.a
3scn.a
3sco.a
3scp.a
3scq.a
3scr.a
3scs.a
3sct.a
3scu.a
3scw.a
4qlj.a
4qlk.a
4qll.a
[1] 2rgl.a
0
0.4 0.5 1.4 0.4 0.4 1.4 0.4 0.3 0.4 0.3 0.4 0.4 0.4 0.5 0.5 0.6 0.4 0.4
[1] 2rgm.a 0.4
0
0.3 1.4 0.5 0.5 1.4 0.4 0.4 0.4 0.3 0.4 0.5 0.4 0.5 0.5 0.7 0.5 0.5
[1] 3ahv.a 0.5 0.3
0
1.4 0.3 0.3 1.3 0.3 0.3 0.2 0.3 0.2 0.4 0.3 0.4 0.4 0.6 0.4 0.4
[1] 3f4v.a 1.4 1.4 1.4
0
1.3 1.3 0.1 1.3 1.4 1.3 1.4 1.3 1.3 1.3 1.4 0.9 1.1 0.9 0.9
[1] 3f5j.a 0.4 0.5 0.3 1.3
0
0.1 1.3 0.3 0.3 0.2 0.3 0.2 0.5 0.2 0.4 0.3 0.6 0.2 0.2
[1] 3f5k.a 0.4 0.5 0.3 1.3 0.1
0
1.3 0.3 0.3 0.2 0.3 0.2 0.5 0.2 0.4 0.3 0.6 0.2 0.2
[1] 3f5l.a 1.4 1.4 1.3 0.1 1.3 1.3
0
1.3 1.4 1.3 1.3 1.3 1.3 1.3 1.4 0.9 1.1 0.9 0.9
[1] 3scn.a 0.4 0.4 0.3 1.3 0.3 0.3 1.3
0
0.2 0.2 0.3 0.2 0.5 0.2 0.3 0.4 0.6 0.4 0.4
[1] 3sco.a 0.3 0.4 0.3 1.4 0.3 0.3 1.4 0.2
0
0.2 0.1 0.2 0.4 0.2 0.4 0.4 0.6 0.4 0.4
[1] 3scp.a 0.4 0.4 0.2 1.3 0.2 0.2 1.3 0.2 0.2
0
0.2 0.1 0.4 0.1 0.3 0.3 0.6 0.3 0.3
[1] 3scq.a 0.3 0.3 0.3 1.4 0.3 0.3 1.3 0.3 0.1 0.2
0
0.2 0.3 0.2 0.4 0.4 0.6 0.4 0.3
[1] 3scr.a 0.4 0.4 0.2 1.3 0.2 0.2 1.3 0.2 0.2 0.1 0.2
0
0.4 0.2 0.3 0.3 0.6 0.3 0.3
[1] 3scs.a 0.4 0.5 0.4 1.3 0.5 0.5 1.3 0.5 0.4 0.4 0.3 0.4
0
0.4 0.5 0.4 0.6 0.4 0.4
[1] 3sct.a 0.4 0.4 0.3 1.3 0.2 0.2 1.3 0.2 0.2 0.1 0.2 0.2 0.4
0
0.3 0.3 0.6 0.3 0.3
[1] 3scu.a 0.5 0.5 0.4 1.4 0.4 0.4 1.4 0.3 0.4 0.3 0.4 0.3 0.5 0.3
0
0.5 0.5 0.5 0.5
[1] 3scw.a 0.5 0.5 0.4 0.9 0.3 0.3 0.9 0.4 0.4 0.3 0.4 0.3 0.4 0.3 0.5
0
0.5 0.3 0.2
[1] 4qlj.a 0.6 0.7 0.6 1.1 0.6 0.6 1.1 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.5 0.5
0
0.6 0.6
[1] 4qlk.a 0.4 0.5 0.4 0.9 0.2 0.2 0.9 0.4 0.4 0.3 0.4 0.3 0.4 0.3 0.5 0.3 0.6
0
0.1
[1] 4qll.a 0.4 0.5 0.4 0.9 0.2 0.2 0.9 0.4 0.4 0.3 0.3 0.3 0.4 0.3 0.5 0.2 0.6 0.1
0
[Binding site full-atom RMSD matrix]







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