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DSBA_PSEAE_21_211

Thiol:disulfide interchange protein DsbA [Thioredoxin family. DsbA subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DSBA_PSEAE):D: Thioredoxin (39:41, 47, 49, 80, 82, 98, 156, 159, 160, 163, 167)39:41, 47, 49, 80, 82, 98, 156, 159, 160, 163, 167

Full PDB list

3h93, 4zl7, 4zl8, 4zl9, 5dch (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
P
3
9
V
4
0
S
4
1
E
4
7
V
4
9
V
8
0
L
8
2
L
9
8
Q
1
5
6
K
1
5
9
A
1
6
0
L
1
6
3
Y
1
6
7
[1]4zl8.a none . . . . . . . . . . . . .
[1]5dch.a 1yo15 . . . . . . . . . . . . .

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

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PDB.ch
A1
P
3
9
V
4
0
S
4
1
E
4
7
V
4
9
V
8
0
L
8
2
L
9
8
Q
1
5
6
K
1
5
9
A
1
6
0
L
1
6
3
Y
1
6
7
[1]4zl8.a . . . . . . . . . . . . .
[1]5dch.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
4zl8.a is apo
5dch.a:1yo
[1] 4zl8.a
-
0.2
[1] 5dch.a -
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
4zl8.a
5dch.a
[1] 4zl8.a
0
.02
[1] 5dch.a .02
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
4zl8.a
5dch.a
[1] 4zl8.a
0
0.2
[1] 5dch.a 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

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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
4zl8.a
5dch.a
[1] 4zl8.a
0
0.6
[1] 5dch.a 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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