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DSBA_ECOLI_20_208

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DSBA_ECOLI):D: Thioredoxin (43, 48:59, 61, 62, 82:84, 112, 113, 116:118)
166:172, 179:183, 187:190, 193, 197
43, 48:59, 61, 62, 82:84, 112, 113, 116:118, 166:172, 179:183, 187:190, 193, 197

Full PDB list

1a2j, 1a2l, 1a2m, 1ac1, 1acv, 1bq7, 1dsb, 1fvj, 1fvk, 1ti1, 1u3a, 2b3s, 2b6m, 3dks, 4tky, 4wet, 4wey, 4wf4, 4wf5, 4zij, 6bqx, 6br4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
4
3
C
4
9
P
5
0
H
5
1
Y
5
3
Q
5
4
F
5
5
E
5
7
V
5
8
L
5
9
I
6
1
S
6
2
F
8
2
M
8
3
K
1
1
7
R
1
6
7
G
1
6
8
V
1
6
9
P
1
7
0
M
1
7
2
Q
1
7
9
L
1
8
0
P
1
8
2
Q
1
8
3
T
1
8
7
N
1
8
9
M
1
9
0
F
1
9
3
Y
1
9
7
[1]1a2m.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ac1.a none . . . L . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1acv.a none . . . S . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1bq7.c none . . . . . . . . . . . . . . . . . . A . . . . . . . . . .
[1]1fvj.a none . . . Y . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3dks.b acePIPFLhseQK68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wet.a wef31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wey.a eg622 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wf4.b wf419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4wf5.a wf4,wf438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4zij.a sfq20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6bqx.a 9ag16 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6br4.a 60l14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2b6m.b none . . A . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4tky.a PFATCDS,PFATCDS100 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4tky.b PFATCDS50 . * . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]1ti1.a d1212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]1u3a.d pe524 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[4]2b3s.a none . . G . . . . . . . . . . . . . . . . . . . . . . . . . .

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
E
4
3
F
4
8
C
4
9
P
5
0
H
5
1
C
5
2
Y
5
3
Q
5
4
F
5
5
E
5
6
E
5
7
V
5
8
L
5
9
I
6
1
S
6
2
F
8
2
M
8
3
G
8
4
F
1
1
2
E
1
1
3
Q
1
1
6
K
1
1
7
T
1
1
8
L
1
6
6
R
1
6
7
G
1
6
8
V
1
6
9
P
1
7
0
A
1
7
1
M
1
7
2
Q
1
7
9
L
1
8
0
N
1
8
1
P
1
8
2
Q
1
8
3
T
1
8
7
S
1
8
8
N
1
8
9
M
1
9
0
F
1
9
3
Y
1
9
7
[1]1a2m.b . . . . * . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ac1.a . . . . L . . . * . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]1acv.a . . . . S . . . * . . . . . . . . . . . . * . . . . . . . . . . . . * . . . . . .
[1]1bq7.c . . . . * . . . * . . . . . . . . . . . . * . . . . . A . . . . . . . . . . * . .
[1]1fvj.a . . . . Y . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3dks.b . . . . * . . * * . . . . . . . . . . . . * . . . . . . . . . . . . . . . . * . .
[1]4wet.a . . . . * . . . * . . . . . . . * . . . . * . . . . . . . . . . . . . . . . . . .
[1]4wey.a . . . . * . . . * . . . . . . . * . . . . * . . . . . . . . . . . . . . . . . . .
[1]4wf4.b . . . . * . . . * . . . . . . . * . . . . * . . . . . . . . . . . . . . . . . . .
[1]4wf5.a . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4zij.a . . . . * . . . * . . . . . . . * . . . . . . . . . . . . . . . . . * . . . . . .
[1]6bqx.a . . . . * . . . * . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]6br4.a . . . . * . . . * . . . . . . . . . . . . * . . * . . . . . . . . . * . . . . . .
[2]2b6m.b . . * A . A . . * . . . . . . . . . . . . . . . . . . . . . . . . . * . . . * . .
[2]4tky.a . . * . . A . * * . . . . . . . . . . . . . . . . . . . . . . . . . * . . . * . .
[2]4tky.b . . * . . A . . * . . . . . . . . . . . . . . . . . . . . . . . . . * . . . * . .
[3]1ti1.a . . * . . A * . . . * . . . . . . . . . . * . . . . . . . . . . . . . . . . . . .
[3]1u3a.d . . * . . A * . . . * . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[4]2b3s.a . . * G * 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
1a2m.b is apo
1ac1.a is apo
1acv.a is apo
1bq7.c is apo
1fvj.a is apo
3dks.b:acePIPFLhseQK
4wet.a:wef
4wey.a:eg6
4wf4.b:wf4
4wf5.a:wf4
4zij.a:sfq
6bqx.a:9ag
6br4.a:60l
2b6m.b is apo
4tky.a:PFATCDS
4tky.b:PFATCDS
1ti1.a:d12
1u3a.d:pe5
2b3s.a is apo
[1] 1a2m.b
-
- - - - 0.2 0 0.1 0 2.0 0.6 0.5 0.5 - 5.8 3.5 2.6 2.8 -
[1] 1ac1.a -
-
- - - 0.1 0.3 0.4 0.3 2.1 0.6 0.5 0.7 - 5.4 2.1 2.7 3.3 -
[1] 1acv.a - -
-
- - 0.1 0.6 0.2 0.7 2.7 0.2 0 0.1 - 4.7 1.6 3.2 3.1 -
[1] 1bq7.c - - -
-
- 0.4 1.8 1.5 1.7 1.7 1.8 0.1 0.3 - 5.5 2.9 2.4 4.2 -
[1] 1fvj.a - - - -
-
0.1 1.9 2.1 2.1 3.7 2.2 2.9 2.6 - 5.8 3.8 5.3 5.9 -
[1] 3dks.b - - - - -
0
2.1 2.2 2.3 4.2 2.8 2.3 1.9 - 5.8 2.2 4.3 5.2 -
[1] 4wet.a - - - - - 0.1
0
0 0.1 2.3 0.7 0.1 0.3 - 7.5 3.8 3.1 2.8 -
[1] 4wey.a - - - - - 0.5 0.1
0
0 2.6 0.6 0.2 0.4 - 6.5 3.6 3.2 2.6 -
[1] 4wf4.b - - - - - 0.2 0 0
0
1.5 0.6 0.2 0.3 - 6.3 3.1 3.2 2.6 -
[1] 4wf5.a - - - - - 0.1 0.2 0.2 0.2
0
0.5 0 0 - 4.8 3.0 3.3 2.8 -
[1] 4zij.a - - - - - 0.3 0.2 0.1 0.3 2.6
0
0.1 0.5 - 7.2 4.2 3.5 2.9 -
[1] 6bqx.a - - - - - 0.1 0.2 0.1 0.1 1.5 0.3
0
0 - 6.8 4.1 3.2 3.4 -
[1] 6br4.a - - - - - 0 0.7 0.5 1.3 3.2 0.2 0.1
0
- 8.5 5.2 3.3 3.4 -
[2] 2b6m.b - - - - - 0.1 2.7 2.7 3.3 3.2 0.8 0.2 0.1
-
1.6 1.6 3.5 3.0 -
[2] 4tky.a - - - - - 0 2.2 1.8 1.7 3.4 2.2 0.5 0.7 -
0.4
0.4 3.5 3.3 -
[2] 4tky.b - - - - - 0 2.5 1.7 1.8 3.7 2.2 0.5 0.6 - 0.5
0.4
3.4 3.1 -
[3] 1ti1.a - - - - - 0.2 1.1 0.5 0.6 1.3 0.5 0 0.1 - 6.4 1.4
0
0.6 -
[3] 1u3a.d - - - - - 0.7 0.4 0.4 0.5 2.3 0.8 1.5 1.2 - 5.1 1.6 0
0
-
[4] 2b3s.a - - - - - 0.6 0.8 0.4 0.8 3.9 0.5 0.2 0.6 - 9.5 1.0 0.4 0.5
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
1a2m.b
1ac1.a
1acv.a
1bq7.c
1fvj.a
3dks.b
4wet.a
4wey.a
4wf4.b
4wf5.a
4zij.a
6bqx.a
6br4.a
2b6m.b
4tky.a
4tky.b
1ti1.a
1u3a.d
2b3s.a
[1] 1a2m.b
0
.07 .15 .16 .09 .15 .10 .12 .10 .09 .10 .08 .14 .29 .27 .26 .32 .33 .39
[1] 1ac1.a .07
0
.09 .15 .07 .16 .07 .08 .05 .08 .10 .06 .12 .27 .28 .27 .30 .31 .42
[1] 1acv.a .15 .09
0
.20 .15 .23 .13 .11 .12 .16 .14 .12 .10 .20 .22 .20 .31 .30 .42
[1] 1bq7.c .16 .15 .20
0
.19 .13 .17 .16 .16 .17 .21 .18 .23 .24 .22 .21 .34 .37 .47
[1] 1fvj.a .09 .07 .15 .19
0
.18 .11 .14 .11 .08 .11 .06 .11 .27 .28 .28 .35 .36 .39
[1] 3dks.b .15 .16 .23 .13 .18
0
.15 .18 .17 .15 .20 .16 .22 .28 .23 .22 .38 .41 .48
[1] 4wet.a .10 .07 .13 .17 .11 .15
0
.05 .06 .10 .07 .06 .12 .28 .29 .29 .33 .33 .41
[1] 4wey.a .12 .08 .11 .16 .14 .18 .05
0
.04 .12 .06 .08 .13 .26 .27 .27 .32 .31 .40
[1] 4wf4.b .10 .05 .12 .16 .11 .17 .06 .04
0
.10 .08 .08 .15 .27 .29 .28 .31 .29 .42
[1] 4wf5.a .09 .08 .16 .17 .08 .15 .10 .12 .10
0
.11 .09 .17 .24 .24 .24 .29 .31 .41
[1] 4zij.a .10 .10 .14 .21 .11 .20 .07 .06 .08 .11
0
.07 .13 .28 .29 .29 .33 .32 .38
[1] 6bqx.a .08 .06 .12 .18 .06 .16 .06 .08 .08 .09 .07
0
.09 .27 .28 .28 .33 .33 .40
[1] 6br4.a .14 .12 .10 .23 .11 .22 .12 .13 .15 .17 .13 .09
0
.26 .30 .28 .40 .40 .40
[2] 2b6m.b .29 .27 .20 .24 .27 .28 .28 .26 .27 .24 .28 .27 .26
0
.08 .07 .33 .33 .41
[2] 4tky.a .27 .28 .22 .22 .28 .23 .29 .27 .29 .24 .29 .28 .30 .08
0
.02 .34 .35 .42
[2] 4tky.b .26 .27 .20 .21 .28 .22 .29 .27 .28 .24 .29 .28 .28 .07 .02
0
.34 .34 .42
[3] 1ti1.a .32 .30 .31 .34 .35 .38 .33 .32 .31 .29 .33 .33 .40 .33 .34 .34
0
.15 .25
[3] 1u3a.d .33 .31 .30 .37 .36 .41 .33 .31 .29 .31 .32 .33 .40 .33 .35 .34 .15
0
.28
[4] 2b3s.a .39 .42 .42 .47 .39 .48 .41 .40 .42 .41 .38 .40 .40 .41 .42 .42 .25 .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
1a2m.b
1ac1.a
1acv.a
1bq7.c
1fvj.a
3dks.b
4wet.a
4wey.a
4wf4.b
4wf5.a
4zij.a
6bqx.a
6br4.a
2b6m.b
4tky.a
4tky.b
1ti1.a
1u3a.d
2b3s.a
[1] 1a2m.b
0
0.5 0.5 0.9 0.5 0.7 0.5 0.6 0.5 0.7 0.6 0.5 0.5 2.1 1.3 1.2 2.9 3.4 3.5
[1] 1ac1.a 0.5
0
0.1 1.0 0.2 0.8 0.4 0.5 0.5 0.8 0.6 0.3 0.3 2.2 1.3 1.3 3.0 3.4 3.5
[1] 1acv.a 0.5 0.1
0
1.0 0.2 0.8 0.5 0.6 0.5 0.8 0.6 0.3 0.3 2.2 1.3 1.3 3.0 3.4 3.5
[1] 1bq7.c 0.9 1.0 1.0
0
1.0 0.9 0.9 1.0 1.0 0.9 1.1 1.0 1.1 2.1 1.3 1.3 2.9 3.4 3.4
[1] 1fvj.a 0.5 0.2 0.2 1.0
0
0.8 0.5 0.6 0.6 0.8 0.6 0.3 0.3 2.1 1.2 1.2 2.9 3.4 3.4
[1] 3dks.b 0.7 0.8 0.8 0.9 0.8
0
0.7 0.8 0.7 0.5 0.9 0.7 0.7 1.9 1.1 1.1 2.8 3.3 3.3
[1] 4wet.a 0.5 0.4 0.5 0.9 0.5 0.7
0
0.2 0.1 0.7 0.3 0.4 0.5 2.3 1.4 1.4 3.0 3.5 3.5
[1] 4wey.a 0.6 0.5 0.6 1.0 0.6 0.8 0.2
0
0.1 0.8 0.2 0.5 0.6 2.3 1.5 1.4 3.0 3.5 3.5
[1] 4wf4.b 0.5 0.5 0.5 1.0 0.6 0.7 0.1 0.1
0
0.8 0.2 0.5 0.6 2.2 1.4 1.4 3.0 3.5 3.5
[1] 4wf5.a 0.7 0.8 0.8 0.9 0.8 0.5 0.7 0.8 0.8
0
0.9 0.8 0.8 2.0 1.1 1.1 2.8 3.3 3.4
[1] 4zij.a 0.6 0.6 0.6 1.1 0.6 0.9 0.3 0.2 0.2 0.9
0
0.5 0.6 2.3 1.5 1.4 3.0 3.5 3.5
[1] 6bqx.a 0.5 0.3 0.3 1.0 0.3 0.7 0.4 0.5 0.5 0.8 0.5
0
0.2 2.2 1.4 1.3 3.0 3.4 3.5
[1] 6br4.a 0.5 0.3 0.3 1.1 0.3 0.7 0.5 0.6 0.6 0.8 0.6 0.2
0
2.2 1.3 1.2 3.0 3.4 3.5
[2] 2b6m.b 2.1 2.2 2.2 2.1 2.1 1.9 2.3 2.3 2.2 2.0 2.3 2.2 2.2
0
1.4 1.4 2.9 3.0 2.8
[2] 4tky.a 1.3 1.3 1.3 1.3 1.2 1.1 1.4 1.5 1.4 1.1 1.5 1.4 1.3 1.4
0
0.1 2.6 3.1 3.1
[2] 4tky.b 1.2 1.3 1.3 1.3 1.2 1.1 1.4 1.4 1.4 1.1 1.4 1.3 1.2 1.4 0.1
0
2.6 3.0 3.1
[3] 1ti1.a 2.9 3.0 3.0 2.9 2.9 2.8 3.0 3.0 3.0 2.8 3.0 3.0 3.0 2.9 2.6 2.6
0
1.3 1.4
[3] 1u3a.d 3.4 3.4 3.4 3.4 3.4 3.3 3.5 3.5 3.5 3.3 3.5 3.4 3.4 3.0 3.1 3.0 1.3
0
1.4
[4] 2b3s.a 3.5 3.5 3.5 3.4 3.4 3.3 3.5 3.5 3.5 3.4 3.5 3.5 3.5 2.8 3.1 3.1 1.4 1.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
1a2m.b
1ac1.a
1acv.a
1bq7.c
1fvj.a
3dks.b
4wet.a
4wey.a
4wf4.b
4wf5.a
4zij.a
6bqx.a
6br4.a
2b6m.b
4tky.a
4tky.b
1ti1.a
1u3a.d
2b3s.a
[1] 1a2m.b
0
0.7 0.7 1.2 0.8 1.2 0.8 0.9 0.9 1.0 1.0 0.9 0.9 2.7 1.7 1.6 4.2 4.4 4.5
[1] 1ac1.a 0.7
0
0.3 1.1 0.4 1.1 0.6 0.7 0.7 1.0 0.8 0.7 0.5 2.6 1.6 1.6 4.0 4.4 4.4
[1] 1acv.a 0.7 0.3
0
1.1 0.3 1.1 0.6 0.8 0.7 0.9 0.8 0.7 0.5 2.6 1.6 1.5 3.9 4.3 4.3
[1] 1bq7.c 1.2 1.1 1.1
0
1.2 1.2 1.3 1.3 1.3 1.2 1.4 1.4 1.5 2.7 1.8 1.7 4.2 4.5 4.6
[1] 1fvj.a 0.8 0.4 0.3 1.2
0
1.1 0.7 0.9 0.8 1.0 1.0 0.7 0.6 2.5 1.6 1.5 4.0 4.4 4.4
[1] 3dks.b 1.2 1.1 1.1 1.2 1.1
0
1.2 1.2 1.2 1.2 1.4 1.4 1.3 2.7 1.7 1.6 4.2 4.4 4.5
[1] 4wet.a 0.8 0.6 0.6 1.3 0.7 1.2
0
0.4 0.4 0.9 0.6 0.8 0.9 2.8 1.8 1.8 4.2 4.5 4.6
[1] 4wey.a 0.9 0.7 0.8 1.3 0.9 1.2 0.4
0
0.2 0.9 0.5 0.9 0.9 2.8 1.9 1.8 4.1 4.4 4.5
[1] 4wf4.b 0.9 0.7 0.7 1.3 0.8 1.2 0.4 0.2
0
0.8 0.5 0.9 1.0 2.8 1.9 1.8 4.2 4.4 4.5
[1] 4wf5.a 1.0 1.0 0.9 1.2 1.0 1.2 0.9 0.9 0.8
0
1.0 1.1 1.0 2.5 1.5 1.5 4.0 4.4 4.3
[1] 4zij.a 1.0 0.8 0.8 1.4 1.0 1.4 0.6 0.5 0.5 1.0
0
1.0 1.1 2.9 1.9 1.9 4.1 4.4 4.5
[1] 6bqx.a 0.9 0.7 0.7 1.4 0.7 1.4 0.8 0.9 0.9 1.1 1.0
0
0.9 2.8 1.8 1.7 4.2 4.5 4.6
[1] 6br4.a 0.9 0.5 0.5 1.5 0.6 1.3 0.9 0.9 1.0 1.0 1.1 0.9
0
2.7 1.7 1.6 4.2 4.5 4.5
[2] 2b6m.b 2.7 2.6 2.6 2.7 2.5 2.7 2.8 2.8 2.8 2.5 2.9 2.8 2.7
0
1.9 2.0 4.2 4.3 3.8
[2] 4tky.a 1.7 1.6 1.6 1.8 1.6 1.7 1.8 1.9 1.9 1.5 1.9 1.8 1.7 1.9
0
0.3 4.0 4.2 4.2
[2] 4tky.b 1.6 1.6 1.5 1.7 1.5 1.6 1.8 1.8 1.8 1.5 1.9 1.7 1.6 2.0 0.3
0
4.0 4.2 4.2
[3] 1ti1.a 4.2 4.0 3.9 4.2 4.0 4.2 4.2 4.1 4.2 4.0 4.1 4.2 4.2 4.2 4.0 4.0
0
1.8 2.0
[3] 1u3a.d 4.4 4.4 4.3 4.5 4.4 4.4 4.5 4.4 4.4 4.4 4.4 4.5 4.5 4.3 4.2 4.2 1.8
0
2.0
[4] 2b3s.a 4.5 4.4 4.3 4.6 4.4 4.5 4.6 4.5 4.5 4.3 4.5 4.6 4.5 3.8 4.2 4.2 2.0 2.0
0
[Binding site full-atom RMSD matrix]







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