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.

CDGT2_BACCI_28_713

Cyclomaltodextrin glucanotransferase [Glycosyl hydrolase 13 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDGT2_BACCI):R: B (211, 212)
D: CBM20 (625:630, 654, 655, 660, 663)
R: E (625:630, 654, 655, 660, 663)
211, 212, 625:630, 654, 655, 660, 663
Metals (Me):Ca

Full PDB list

1cdg, 1cgv, 1cgw, 1cgx, 1cgy, 1cxe, 1cxf, 1cxh, 1cxi, 1cxk, 1cxl, 1d3c, 1dtu, 1eo5, 1eo7, 1kck, 1kcl, 1ot1, 1ot2, 1pez, 1pj9, 1tcm, 2cxg, 2dij (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
T
2
1
2
T
6
2
5
A
6
2
6
L
6
2
7
G
6
2
8
Q
6
2
9
N
6
3
0
N
6
5
4
Q
6
5
5
Y
6
6
0
W
6
6
3
[1]1cxf.a acx66 . . . . . . . . . . . Ca
[1]1cxl.a glc.g4d22 . . . . . . . . . . . Ca
[1]1d3c.a glc.glc.glc.glc.glc.glc.glc.glc88 . . . . . . . . . . . Ca
[1]1dtu.a bgc.agc.agc.agc.agc56 . . . . . . . . . . . Ca
[1]1eo5.a glc.glc.glc.glc45 . . . . . . . . . . . Ca
[1]1kck.a glc.glc.glc34 . . . . . . . . . . . Ca
[1]1kcl.a mal23 . . . . . . . . . . . Ca
[1]1ot1.a bgc.agc.agc.agc45 . . . . . . . . . . . Ca
[1]1pj9.a glc.glc.glc34 S . . . . . . . . . . Ca
[1]1tcm.b none . . . . . . . . . . . Ca
[1]2cxg.a glc.glc23 . . . . . . . . . . . Ca
[1]2dij.a glc.glc.glc.glc.glc56 . . . . . . . . . . . Ca

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
S
2
1
1
T
2
1
2
T
6
2
5
A
6
2
6
L
6
2
7
G
6
2
8
Q
6
2
9
N
6
3
0
N
6
5
4
Q
6
5
5
Y
6
6
0
W
6
6
3
[1]1cxf.a . . . . . . . . . . . . Ca
[1]1cxl.a . . . . . . . . . . . . Ca
[1]1d3c.a . . . . . . . . . . . . Ca
[1]1dtu.a . . . . . . . . . . . . Ca
[1]1eo5.a . . . . * . . . . . . . Ca
[1]1kck.a . . . . . . . . . . . . Ca
[1]1kcl.a . . . . . . . . . . . . Ca
[1]1ot1.a . . . . . . . . . . . . Ca
[1]1pj9.a . S . . . . . . . . . . Ca
[1]1tcm.b . . . . . . . . . . . . Ca
[1]2cxg.a . . . . * . . . . . . . Ca
[1]2dij.a . . . . . . . . . . . . Ca

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
1cxf.a:acx
1cxl.a:glc.g4d
1d3c.a:glc.glc.glc.glc.glc.glc.glc.glc
1dtu.a:bgc.agc.agc.agc.agc
1eo5.a:glc.glc.glc.glc
1kck.a:glc.glc.glc
1kcl.a:mal
1ot1.a:bgc.agc.agc.agc
1pj9.a:glc.glc.glc
1tcm.b is apo
2cxg.a:glc.glc
2dij.a:glc.glc.glc.glc.glc
[1] 1cxf.a
0
0 0 0 0 0 0 0 0 - 0.1 0
[1] 1cxl.a 0.1
0
0 0.1 0 0.2 0 0 0 - 0.2 0
[1] 1d3c.a 0.3 0
0
0 0 0.1 0 0 0 - 0.1 0
[1] 1dtu.a 0.1 0 0
0
0 0.1 0 0 0 - 0.1 0
[1] 1eo5.a 0.7 0 0.1 0.2
0
0.5 0 0.1 0.1 - 0.2 0.1
[1] 1kck.a 0.1 0 0 0 0
0
0 0 0 - 0 0.1
[1] 1kcl.a 0 0 0 0 0 0.1
0
0 0 - 0.1 0.1
[1] 1ot1.a 0.3 0 0 0.1 0 0.2 0
0
0 - 0.2 0.2
[1] 1pj9.a 0.2 0 0 0.1 0.1 0.2 0 0
0
- 0.2 0
[1] 1tcm.b 0.3 0.3 0.3 0.3 0.3 0.3 0.1 0.3 0.3
-
0.3 0.3
[1] 2cxg.a 0.7 0 0.2 0.1 0 0.4 0 0.1 0.1 -
0
0.2
[1] 2dij.a 0.2 0 0 0 0 0.1 0 0 0 - 0.1
0
[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
1cxf.a
1cxl.a
1d3c.a
1dtu.a
1eo5.a
1kck.a
1kcl.a
1ot1.a
1pj9.a
1tcm.b
2cxg.a
2dij.a
[1] 1cxf.a
0
.03 .04 .03 .08 .02 .03 .07 .05 .03 .07 .03
[1] 1cxl.a .03
0
.03 .01 .05 .03 .03 .03 .02 .02 .07 .02
[1] 1d3c.a .04 .03
0
.02 .06 .04 .03 .04 .03 .04 .06 .01
[1] 1dtu.a .03 .01 .02
0
.06 .03 .02 .04 .03 .03 .06 .01
[1] 1eo5.a .08 .05 .06 .06
0
.08 .07 .05 .05 .07 .03 .05
[1] 1kck.a .02 .03 .04 .03 .08
0
.03 .05 .05 .03 .05 .03
[1] 1kcl.a .03 .03 .03 .02 .07 .03
0
.04 .04 .03 .08 .03
[1] 1ot1.a .07 .03 .04 .04 .05 .05 .04
0
.03 .05 .05 .03
[1] 1pj9.a .05 .02 .03 .03 .05 .05 .04 .03
0
.03 .07 .02
[1] 1tcm.b .03 .02 .04 .03 .07 .03 .03 .05 .03
0
.08 .03
[1] 2cxg.a .07 .07 .06 .06 .03 .05 .08 .05 .07 .08
0
.05
[1] 2dij.a .03 .02 .01 .01 .05 .03 .03 .03 .02 .03 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1cxf.a
1cxl.a
1d3c.a
1dtu.a
1eo5.a
1kck.a
1kcl.a
1ot1.a
1pj9.a
1tcm.b
2cxg.a
2dij.a
[1] 1cxf.a
0
0.2 0.3 0.4 0.3 0.4 0.3 0.3 0.3 0.7 0.5 0.4
[1] 1cxl.a 0.2
0
0.2 0.3 0.1 0.3 0.2 0.1 0.2 0.7 0.4 0.3
[1] 1d3c.a 0.3 0.2
0
0.2 0.3 0.3 0.4 0.3 0.3 0.7 0.4 0.2
[1] 1dtu.a 0.4 0.3 0.2
0
0.3 0.2 0.4 0.4 0.4 0.6 0.3 0.2
[1] 1eo5.a 0.3 0.1 0.3 0.3
0
0.3 0.2 0.1 0.2 0.7 0.4 0.3
[1] 1kck.a 0.4 0.3 0.3 0.2 0.3
0
0.4 0.3 0.4 0.6 0.3 0.3
[1] 1kcl.a 0.3 0.2 0.4 0.4 0.2 0.4
0
0.1 0.2 0.7 0.5 0.4
[1] 1ot1.a 0.3 0.1 0.3 0.4 0.1 0.3 0.1
0
0.2 0.7 0.4 0.4
[1] 1pj9.a 0.3 0.2 0.3 0.4 0.2 0.4 0.2 0.2
0
0.7 0.5 0.4
[1] 1tcm.b 0.7 0.7 0.7 0.6 0.7 0.6 0.7 0.7 0.7
0
0.5 0.6
[1] 2cxg.a 0.5 0.4 0.4 0.3 0.4 0.3 0.5 0.4 0.5 0.5
0
0.3
[1] 2dij.a 0.4 0.3 0.2 0.2 0.3 0.3 0.4 0.4 0.4 0.6 0.3
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
1cxf.a
1cxl.a
1d3c.a
1dtu.a
1eo5.a
1kck.a
1kcl.a
1ot1.a
1pj9.a
1tcm.b
2cxg.a
2dij.a
[1] 1cxf.a
0
0.4 0.6 0.6 0.6 1.0 1.0 1.0 0.6 1.1 0.8 0.6
[1] 1cxl.a 0.4
0
0.4 0.4 0.4 0.9 0.9 0.9 0.5 0.9 0.6 0.5
[1] 1d3c.a 0.6 0.4
0
0.4 0.5 0.8 0.8 0.8 0.3 0.9 0.6 0.2
[1] 1dtu.a 0.6 0.4 0.4
0
0.6 0.8 0.9 0.9 0.5 0.9 0.5 0.4
[1] 1eo5.a 0.6 0.4 0.5 0.6
0
0.9 0.9 0.8 0.5 1.0 0.7 0.4
[1] 1kck.a 1.0 0.9 0.8 0.8 0.9
0
0.4 0.3 0.8 1.2 0.9 0.8
[1] 1kcl.a 1.0 0.9 0.8 0.9 0.9 0.4
0
0.2 0.7 1.3 1.0 0.9
[1] 1ot1.a 1.0 0.9 0.8 0.9 0.8 0.3 0.2
0
0.7 1.2 1.0 0.8
[1] 1pj9.a 0.6 0.5 0.3 0.5 0.5 0.8 0.7 0.7
0
0.9 0.7 0.4
[1] 1tcm.b 1.1 0.9 0.9 0.9 1.0 1.2 1.3 1.2 0.9
0
0.9 0.9
[1] 2cxg.a 0.8 0.6 0.6 0.5 0.7 0.9 1.0 1.0 0.7 0.9
0
0.6
[1] 2dij.a 0.6 0.5 0.2 0.4 0.4 0.8 0.9 0.8 0.4 0.9 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...