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DEOR_BACSU_55_313

Deoxyribonucleoside regulator [SorC transcriptional regulatory family]

Composition of the binding site

Protein chains monomer
A1 (DEOR_BACSU):87, 115:119, 141, 208, 210, 211, 216, 217, 239, 242, 282, 28387, 115:119, 141, 208, 210, 211, 216, 217, 239, 242, 282, 283

Full PDB list

4oqp, 4oqq

Pocket contact map

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PDB.ch
   
ligand
A1
Y
8
7
S
1
1
5
W
1
1
6
G
1
1
7
T
1
1
8
T
1
1
9
K
1
4
1
T
2
0
8
G
2
1
0
T
2
1
1
D
2
3
9
S
2
4
2
R
2
8
2
K
2
8
3
[1]4oqp.a ped12 . . . . . . * . . . . . . .
[1]4oqq.a bcn11 . . . . . . . . . . . . . .

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
Y
8
7
S
1
1
5
W
1
1
6
G
1
1
7
T
1
1
8
T
1
1
9
K
1
4
1
T
2
0
8
G
2
1
0
T
2
1
1
A
2
1
6
L
2
1
7
D
2
3
9
S
2
4
2
R
2
8
2
K
2
8
3
[1]4oqp.a . . . . . . * . . . . . . . . .
[1]4oqq.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
4oqp.a:ped
4oqq.a:bcn
[1] 4oqp.a
0.6
0.3
[1] 4oqq.a 1.1
0.2
[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
4oqp.a
4oqq.a
[1] 4oqp.a
0
.04
[1] 4oqq.a .04
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
4oqp.a
4oqq.a
[1] 4oqp.a
0
1.1
[1] 4oqq.a 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
4oqp.a
4oqq.a
[1] 4oqp.a
0
1.4
[1] 4oqq.a 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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