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DCTP_DESAG_28_340

Solute-binding protein Dde_0634 [Bacterial solute-binding protein 7 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DCTP_DESAG):R: Indole-3-acetate binding (210, 211, 213)
39, 40, 44:46, 96, 99, 149, 172, 193, 214, 235, 237
39, 40, 44:46, 96, 99, 149, 172, 193, 210, 211, 213, 214, 235, 237

Full PDB list

4nap, 4pgn, 4pgp

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
3
9
P
4
0
T
4
4
F
4
5
P
4
6
S
9
6
Y
9
9
S
1
4
9
R
1
7
2
M
1
9
3
T
2
1
0
S
2
1
1
D
2
1
3
V
2
1
4
Y
2
3
5
F
2
3
7
[1]4nap.a dtr15 . . . . . . . . . * . . . . . .
[1]4pgn.a 3io15 . . . . . . . . . . . . . . . .
[1]4pgp.a iac13 . . . . . . . . . . . . . . . .

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
F
3
9
P
4
0
T
4
4
F
4
5
P
4
6
S
9
6
Y
9
9
S
1
4
9
R
1
7
2
M
1
9
3
T
2
1
0
S
2
1
1
D
2
1
3
V
2
1
4
Y
2
3
5
F
2
3
7
[1]4nap.a . . . . . . . . . * . . . . . .
[1]4pgn.a . . . . . . . . . . . . . . . .
[1]4pgp.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
4nap.a:dtr
4pgn.a:3io
4pgp.a:iac
[1] 4nap.a
0.3
0.1 0
[1] 4pgn.a 0.1
0.1
0
[1] 4pgp.a 0.3 0.1
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
4nap.a
4pgn.a
4pgp.a
[1] 4nap.a
0
.01 .01
[1] 4pgn.a .01
0
.01
[1] 4pgp.a .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
4nap.a
4pgn.a
4pgp.a
[1] 4nap.a
0
0.1 0.2
[1] 4pgn.a 0.1
0
0.2
[1] 4pgp.a 0.2 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
4nap.a
4pgn.a
4pgp.a
[1] 4nap.a
0
0.5 0.2
[1] 4pgn.a 0.5
0
0.5
[1] 4pgp.a 0.2 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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