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DHGB_ACICA_25_478

Quinoprotein glucose dehydrogenase B [PQQ oxidoreductase GdhB family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DHGB_ACICA):R: PQQ (252, 253)
R: PQQ (430, 432)
100, 168, 192, 255, 270:272, 367, 370, 372, 374, 400, 401
100, 168, 192, 252, 253, 255, 270:272, 367, 370, 372, 374, 400, 401, 430, 432
Metals (Me):Ca

Full PDB list

1c9u, 1cq1, 1cru, 1qbi, 5min (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
1
0
0
H
1
6
8
R
2
5
2
N
2
5
3
Q
2
5
5
Q
2
7
0
G
2
7
1
P
2
7
2
Y
3
6
7
W
3
7
0
T
3
7
2
A
3
7
4
L
4
0
0
K
4
0
1
R
4
3
0
R
4
3
2
[1]1cq1.b pqq24 . . . . . . . . . . . . . . . . Ca
[1]1cru.a pqq.hdn27 . . . . . . . . . . . . . . . . Ca
[1]5min.a ca1 . . . . . . . . . . . . . . . . Ca
[1]5min.b none . . . . . . . . . . . . . . . . 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
Q
1
0
0
H
1
6
8
Q
1
9
2
R
2
5
2
N
2
5
3
Q
2
5
5
Q
2
7
0
G
2
7
1
P
2
7
2
Y
3
6
7
W
3
7
0
T
3
7
2
A
3
7
4
L
4
0
0
K
4
0
1
R
4
3
0
R
4
3
2
[1]1cq1.b . . . . . . . . . . . . . . . . . Ca
[1]1cru.a . . . . . . . . . . . . . . . . . Ca
[1]5min.a . . . . . . . . . . . . . . . . . Ca
[1]5min.b . . . . . . . . . . . . . . . . . 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
1cq1.b:pqq
1cru.a:pqq.hdn
5min.a:ca
5min.b is apo
[1] 1cq1.b
0.1
0.1 0 -
[1] 1cru.a 0.1
0
0 -
[1] 5min.a 0.5 0.4
0
-
[1] 5min.b 0.6 0.3 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
1cq1.b
1cru.a
5min.a
5min.b
[1] 1cq1.b
0
.01 .03 .03
[1] 1cru.a .01
0
.03 .03
[1] 5min.a .03 .03
0
0
[1] 5min.b .03 .03 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1cq1.b
1cru.a
5min.a
5min.b
[1] 1cq1.b
0
0.1 0.2 0.2
[1] 1cru.a 0.1
0
0.3 0.2
[1] 5min.a 0.2 0.3
0
0.1
[1] 5min.b 0.2 0.2 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

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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
1cq1.b
1cru.a
5min.a
5min.b
[1] 1cq1.b
0
0.3 0.8 0.8
[1] 1cru.a 0.3
0
0.8 0.8
[1] 5min.a 0.8 0.8
0
0.5
[1] 5min.b 0.8 0.8 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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