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ACRB_ECOLI_1_39

Multidrug efflux pump subunit AcrB [Resistance-nodulation-cell division (RND) (TC 2.A.6) family]

Composition of the binding site

Protein chains homodimer
A1 (ACRB_ECOLI):9, 10, 13, 17, 20, 21, 363, 495, 4969, 10, 13, 17, 20, 21, 363, 495, 496
A2 (ACRB_ECOLI):875, 878, 879, 881, 882, 885, 886, 894:896, 899, 902, 950, 1030, 1033:1035875, 878, 879, 881, 882, 885, 886, 894:896, 899, 902, 950, 1030, 1033:1035

Full PDB list

1iwg, 1oye, 1t9t, 1t9u, 1t9w, 1t9x, 2dhh, 2dr6, 2drd, 2gif, 2hqf, 2hqg, 2i6w, 2j8s, 2rdd, 3aoa, 3aob, 3aoc, 3aod, 3d9b, 3noc, 3nog, 3w9h, 4c48, 4dx5, 4dx6, 4dx7, 4k7q, 4u8v, 4u8y, 4u95, 4u96, 4zlj, 4zll, 5jmn, 5nc5, 5yil (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
P
9
W
1
3
I
1
7
L
2
1
I
8
8
2
F
8
8
5
L
8
8
6
S
8
9
4
W
8
9
5
S
8
9
6
F
8
9
9
M
9
0
2
K
9
5
0
R
1
0
3
0
F
1
0
3
3
[1]4dx5.a d10,d10,d1232 . . . . . . . . . . . . . . .
[1]4dx5.b c14,oct,oct30 . . . . . . . . . . . . . . .
[1]4dx5.c d12,oct,oct28 . . . . . . . . . . . . . . .
[1]4dx6.c none . . . . . . . . . . . . . . .
[1]4dx7.b d10,d1222 . . . . . . . . . . . . . . .
[1]5jmn.a hex,pty56 . . . . . . . . . . . . . . .
[1]5jmn.b oct,pty58 . . . . . . . . . . . . . . .
[1]5jmn.c d1212 . . . . . . . . . . . . . . .

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 A2
P
9
I
1
0
W
1
3
I
1
7
M
2
0
L
2
1
R
3
6
3
T
4
9
5
M
4
9
6
S
8
7
5
A
8
7
8
I
8
7
9
L
8
8
1
I
8
8
2
F
8
8
5
L
8
8
6
S
8
9
4
W
8
9
5
S
8
9
6
F
8
9
9
M
9
0
2
K
9
5
0
R
1
0
3
0
F
1
0
3
3
S
1
0
3
4
R
1
0
3
5
[1]4dx5.a . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]4dx5.b . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]4dx5.c . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dx6.c . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dx7.b . . . . . . . . . . . . . . . . . . . . . . . . . *
[1]5jmn.a . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5jmn.b . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]5jmn.c . . . . . . . . . . . . . . . . . . . . . . . . . -

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
4dx5.a:d10,d12
4dx5.b:c14,oct
4dx5.c:d12,oct
4dx6.c is apo
4dx7.b:d10,d12
5jmn.a:hex,pty
5jmn.b:oct,pty
5jmn.c:d12
[1] 4dx5.a
0
0 0.1 - 0.2 0 0.1 0
[1] 4dx5.b 0.1
0
0.1 - 0 0.2 0.1 0
[1] 4dx5.c 0 0
0
- 0 0 0.2 0
[1] 4dx6.c 0 0.1 0.6
-
0.3 0.1 0.7 0
[1] 4dx7.b 0.3 0.1 0.1 -
0
0.6 2.6 0
[1] 5jmn.a 0 0 0.2 - 0.2
0
0.1 0
[1] 5jmn.b 0.3 0 0.1 - 0 0.1
0
0
[1] 5jmn.c 0 0 0.2 - 0 0 0.2
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
4dx5.a
4dx5.b
4dx5.c
4dx6.c
4dx7.b
5jmn.a
5jmn.b
5jmn.c
[1] 4dx5.a
0
.02 .01 .03 .11 .01 .02 .02
[1] 4dx5.b .02
0
.02 .05 .09 .02 0 .02
[1] 4dx5.c .01 .02
0
.03 .10 .02 .02 .02
[1] 4dx6.c .03 .05 .03
0
.12 .04 .05 .05
[1] 4dx7.b .11 .09 .10 .12
0
.11 .09 .11
[1] 5jmn.a .01 .02 .02 .04 .11
0
.02 .01
[1] 5jmn.b .02 0 .02 .05 .09 .02
0
.02
[1] 5jmn.c .02 .02 .02 .05 .11 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
4dx5.a
4dx5.b
4dx5.c
4dx6.c
4dx7.b
5jmn.a
5jmn.b
5jmn.c
[1] 4dx5.a
0
2.0 0.8 0.8 2.0 0.3 2.2 0.7
[1] 4dx5.b 2.0
0
2.5 2.3 0.5 2.1 0.3 2.3
[1] 4dx5.c 0.8 2.5
0
0.8 2.6 0.9 2.7 0.6
[1] 4dx6.c 0.8 2.3 0.8
0
2.3 0.8 2.4 0.5
[1] 4dx7.b 2.0 0.5 2.6 2.3
0
2.1 0.4 2.4
[1] 5jmn.a 0.3 2.1 0.9 0.8 2.1
0
2.2 0.6
[1] 5jmn.b 2.2 0.3 2.7 2.4 0.4 2.2
0
2.5
[1] 5jmn.c 0.7 2.3 0.6 0.5 2.4 0.6 2.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
4dx5.a
4dx5.b
4dx5.c
4dx6.c
4dx7.b
5jmn.a
5jmn.b
5jmn.c
[1] 4dx5.a
0
2.3 1.1 1.2 2.4 0.9 2.4 1.1
[1] 4dx5.b 2.3
0
2.7 2.5 0.8 2.4 0.9 2.5
[1] 4dx5.c 1.1 2.7
0
0.9 2.9 1.3 3.0 0.8
[1] 4dx6.c 1.2 2.5 0.9
0
2.6 1.2 2.7 0.9
[1] 4dx7.b 2.4 0.8 2.9 2.6
0
2.5 0.8 2.7
[1] 5jmn.a 0.9 2.4 1.3 1.2 2.5
0
2.5 1.1
[1] 5jmn.b 2.4 0.9 3.0 2.7 0.8 2.5
0
2.8
[1] 5jmn.c 1.1 2.5 0.8 0.9 2.7 1.1 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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