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CDGT_BACS0_28_713

Cyclomaltodextrin glucanotransferase [Glycosyl hydrolase 13 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDGT_BACS0):R: A1 (74, 116, 121, 125, 127, 128)
R: Substrate binding (127, 128)
R: B (167, 170, 210, 221:224)
R: Substrate binding (221:223)
R: A2 (254, 256:260, 284:286, 354, 355, 397, 398, 402)
R: Substrate binding (259, 260)
74, 116, 121, 125, 127, 128, 167, 170, 210, 221:224, 254, 256:260, 284:286, 354, 355, 397, 398, 402
Metals (Me):Ca

Full PDB list

1d7f, 1ded, 1i75, 1pam, 1ukq, 1uks, 1ukt, 1v3j, 1v3k, 1v3l, 1v3m (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
R
7
4
Y
1
1
6
N
1
2
1
H
1
2
5
Y
1
2
7
W
1
2
8
H
1
6
7
F
2
1
0
L
2
2
1
Y
2
2
2
D
2
2
3
L
2
2
4
D
2
5
6
A
2
5
7
K
2
5
9
H
2
6
0
E
2
8
4
F
2
8
6
H
3
5
4
D
3
5
5
D
3
9
8
R
4
0
2
[1]1d7f.b none . . . . . . . . . . . . . . . N . . . . . . Ca
[1]1ded.b qps44 . . . . . . . . . . . . . . . N . . . . . . Ca
[1]1i75.b noj11 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1pam.a none . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1ukq.a glc.aci.g6d.bgc44 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1ukq.b glc.aci.g6d.glc44 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1uks.a glc.aci-gal.gld44 . . . . . . . L . . . . . . . . . L . . . . Ca
[1]1ukt.b aci-gal.glc.gld44 . . . . L . . . . . . . . . . . . . . . . . Ca
[1]1v3l.b glc.aci.gld.glc44 . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1v3m.a glc.aci-gal.gld44 . . . . . . . . . . . . . . . . . . . . . . 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
R
7
4
Y
1
1
6
N
1
2
1
H
1
2
5
Y
1
2
7
W
1
2
8
H
1
6
7
P
1
7
0
F
2
1
0
L
2
2
1
Y
2
2
2
D
2
2
3
L
2
2
4
R
2
5
4
D
2
5
6
A
2
5
7
V
2
5
8
K
2
5
9
H
2
6
0
E
2
8
4
W
2
8
5
F
2
8
6
H
3
5
4
D
3
5
5
N
3
9
7
D
3
9
8
R
4
0
2
[1]1d7f.b . . . . . . . . . . . . . . . . . . N . . . . . . . . Ca
[1]1ded.b . . . . . . . . . . . . . . . . . . N . . . . . . . . Ca
[1]1i75.b . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1pam.a . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1ukq.a . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1ukq.b . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1uks.a . . . . . . . . L . . . . . . . . . . . . L . . . . . Ca
[1]1ukt.b . . . . L . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1v3l.b . . . . . . . . . . . . . . . . . . . . . . . . . . . Ca
[1]1v3m.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1d7f.b is apo
1ded.b:qps
1i75.b:noj
1pam.a is apo
1ukq.a:glc.aci.g6d.bgc
1ukq.b:glc.aci.g6d.glc
1uks.a:glc.aci-gal.gld
1ukt.b:aci-gal.glc.gld
1v3l.b:glc.aci.gld.glc
1v3m.a:glc.aci-gal.gld
[1] 1d7f.b
-
0.2 0 - 0 0.1 0 0.1 0.5 0
[1] 1ded.b -
0
0.1 - 0.8 0.9 0.9 0.2 0.7 1.0
[1] 1i75.b - 0.2
0
- 0.1 0.1 0.1 0 0.7 0.1
[1] 1pam.a - 0.3 0
-
0.1 0 0.1 0 0.3 0.2
[1] 1ukq.a - 0.2 0 -
0
0 0 0 0.4 0.1
[1] 1ukq.b - 0.4 0 - 0
0
0 0.1 0.6 0.1
[1] 1uks.a - 0.3 0 - 0 0.2
0
0.1 0.6 0.1
[1] 1ukt.b - 0.1 0.1 - 0.1 0 0
0
0.2 0
[1] 1v3l.b - 0.2 0.1 - 0.7 0.1 0.2 0
0
0.6
[1] 1v3m.a - 0.4 0 - 0.1 0.1 0.2 0 0.6
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
1d7f.b
1ded.b
1i75.b
1pam.a
1ukq.a
1ukq.b
1uks.a
1ukt.b
1v3l.b
1v3m.a
[1] 1d7f.b
0
.07 .02 .02 .01 .01 .03 .02 .06 .03
[1] 1ded.b .07
0
.06 .07 .07 .07 .07 .06 .07 .07
[1] 1i75.b .02 .06
0
.01 .03 .01 .02 .03 .06 .01
[1] 1pam.a .02 .07 .01
0
.02 .01 .02 .01 .04 .02
[1] 1ukq.a .01 .07 .03 .02
0
.01 .03 .01 .06 .03
[1] 1ukq.b .01 .07 .01 .01 .01
0
.02 .02 .06 .02
[1] 1uks.a .03 .07 .02 .02 .03 .02
0
.03 .06 .02
[1] 1ukt.b .02 .06 .03 .01 .01 .02 .03
0
.05 .03
[1] 1v3l.b .06 .07 .06 .04 .06 .06 .06 .05
0
.06
[1] 1v3m.a .03 .07 .01 .02 .03 .02 .02 .03 .06
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

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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
1d7f.b
1ded.b
1i75.b
1pam.a
1ukq.a
1ukq.b
1uks.a
1ukt.b
1v3l.b
1v3m.a
[1] 1d7f.b
0
0.4 0.2 0.2 0.2 0.2 0.2 0.4 0.5 0.3
[1] 1ded.b 0.4
0
0.4 0.5 0.5 0.4 0.5 0.6 0.5 0.4
[1] 1i75.b 0.2 0.4
0
0.1 0.2 0.1 0.2 0.3 0.5 0.2
[1] 1pam.a 0.2 0.5 0.1
0
0.1 0.2 0.2 0.4 0.5 0.2
[1] 1ukq.a 0.2 0.5 0.2 0.1
0
0.2 0.2 0.4 0.5 0.2
[1] 1ukq.b 0.2 0.4 0.1 0.2 0.2
0
0.2 0.3 0.4 0.2
[1] 1uks.a 0.2 0.5 0.2 0.2 0.2 0.2
0
0.4 0.5 0.3
[1] 1ukt.b 0.4 0.6 0.3 0.4 0.4 0.3 0.4
0
0.5 0.4
[1] 1v3l.b 0.5 0.5 0.5 0.5 0.5 0.4 0.5 0.5
0
0.5
[1] 1v3m.a 0.3 0.4 0.2 0.2 0.2 0.2 0.3 0.4 0.5
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

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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
1d7f.b
1ded.b
1i75.b
1pam.a
1ukq.a
1ukq.b
1uks.a
1ukt.b
1v3l.b
1v3m.a
[1] 1d7f.b
0
0.5 0.5 0.8 0.8 0.7 0.7 0.8 0.8 0.7
[1] 1ded.b 0.5
0
0.7 0.9 0.9 0.8 0.8 0.9 0.8 0.8
[1] 1i75.b 0.5 0.7
0
0.7 0.6 0.4 0.7 0.7 0.8 0.6
[1] 1pam.a 0.8 0.9 0.7
0
0.6 0.7 0.7 0.8 0.8 0.6
[1] 1ukq.a 0.8 0.9 0.6 0.6
0
0.6 0.6 0.8 0.8 0.4
[1] 1ukq.b 0.7 0.8 0.4 0.7 0.6
0
0.8 0.8 0.8 0.6
[1] 1uks.a 0.7 0.8 0.7 0.7 0.6 0.8
0
0.9 0.8 0.5
[1] 1ukt.b 0.8 0.9 0.7 0.8 0.8 0.8 0.9
0
0.8 0.8
[1] 1v3l.b 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8
0
0.8
[1] 1v3m.a 0.7 0.8 0.6 0.6 0.4 0.6 0.5 0.8 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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