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ACRB_ECOLI_1_1048_ampicillin

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

Composition of the binding site

Protein chains monomer
A1 (ACRB_ECOLI):29, 30, 96:99, 382, 384:388, 443, 446, 447, 450, 451, 454, 455, 457:461, 468, 472, 475, 476, 478, 479, 482, 866:876, 879, 882, 883, 886, 88729, 30, 96:99, 382, 384:388, 443, 446, 447, 450, 451, 454, 455, 457:461, 468, 472, 475, 476, 478, 479, 482, 866:876, 879, 882, 883, 886, 887

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, 5en5, 5eno, 5enp, 5enq, 5enr, 5ens, 5ent, 5jmn, 5nc5, 5yil (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
2
9
S
9
6
G
9
7
A
3
8
4
A
3
8
5
F
3
8
6
G
3
8
7
F
3
8
8
M
4
4
7
S
4
5
0
A
4
5
1
V
4
5
4
A
4
5
7
F
4
5
8
F
4
5
9
R
4
6
8
I
4
7
2
V
4
7
5
S
4
7
6
N
8
7
1
Q
8
7
2
S
8
7
5
L
8
7
6
I
8
7
9
V
8
8
3
[1]1t9u.a cpf24 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1t9w.a nfn29 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1t9x.a et24 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2j8s.c lmt,lmt70 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2rdd.a aic,aic48 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dx5.c d10,d12,dd9,oct39 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4dx7.c d10,d1222 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k7q.a zld24 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jmn.a ete,lmt49 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5jmn.c d12,pty62 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nc5.a d10,d10,dd925 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nc5.c d10,d12,d12,dd9,dd9,dd943 . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2dr6.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4u8v.b lmt35 . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5jmn.b d1010 . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5nc5.b d10,d10,d12,dd9,dd9,lmt57 . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5yil.b none . . . . . . . . . . . . . . . . . . . S 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
K
2
9
L
3
0
S
9
6
G
9
7
T
9
8
D
9
9
V
3
8
2
A
3
8
4
A
3
8
5
F
3
8
6
G
3
8
7
F
3
8
8
V
4
4
3
A
4
4
6
M
4
4
7
S
4
5
0
A
4
5
1
V
4
5
4
P
4
5
5
A
4
5
7
F
4
5
8
F
4
5
9
G
4
6
0
G
4
6
1
R
4
6
8
I
4
7
2
V
4
7
5
S
4
7
6
M
4
7
8
A
4
7
9
V
4
8
2
E
8
6
6
R
8
6
7
L
8
6
8
S
8
6
9
G
8
7
0
N
8
7
1
Q
8
7
2
A
8
7
3
P
8
7
4
S
8
7
5
L
8
7
6
I
8
7
9
I
8
8
2
V
8
8
3
L
8
8
6
C
8
8
7
[1]1t9u.a . . . . . . . . . . . . . . . . . . . . * * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1t9w.a . . . . . . . . . * . . . . . * . . . . * * . . . . . . . . . . . . . . . . . . * . . . . . .
[1]1t9x.a . . . . . . . . . . . . . . . . . . . . * * . . . . . . . . . . . . . . * . . . . . . . . . .
[1]2j8s.c . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2rdd.a . . . . . . . . . * . . . . . . . . . . * . . . * * . . . . . . * . . . . . . . * . . . . . .
[1]4dx5.c . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4dx7.c . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4k7q.a . . . . . . . . . * . . . . . . . . . . * * . . * . . . . . . - - - . . . . . . . . . . . . .
[1]5jmn.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]5jmn.c . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]5nc5.a . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . .
[1]5nc5.c . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[2]2dr6.a * . . * . . . . . * . . . * . . . . . . . . . . * * . . . . . . . . . . * * . . . . * . . . .
[2]4u8v.b . . . * . . . . . * . . . . . . . . . . . . . . . * . . . . . . . . . . * * . * * * * . . . .
[2]5jmn.b . . . * . . . . . * . . . * . . . . . . . . . . * * . . . . . . . . . . * * . . * * * . . . .
[2]5nc5.b . . . * . . . . . . . . . * . . . . . . . . . . . * . . . . . . . . . . * * * * . * * . . . .
[2]5yil.b * . . * . . . . . . . . . * . . . . . . * . . . * * . . . . . . . - - - S G * * . . * . . . .

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
1t9u.a:cpf
1t9w.a:nfn
1t9x.a:et
2j8s.c:lmt
2rdd.a:aic
4dx5.c:d10,d12,dd9,oct
4dx7.c:d10,d12
4k7q.a:zld
5jmn.a:ete,lmt
5jmn.c:d12,pty
5nc5.a:d10,dd9
5nc5.c:d10,d12,dd9
2dr6.a is apo
4u8v.b:lmt
5jmn.b:d10
5nc5.b:d10,d12,dd9,lmt
5yil.b is apo
[1] 1t9u.a
0
0.6 0.1 1.7 1.9 1.1 0.4 0.1 0 1.1 0.9 0.5 - 1.2 0.9 2.4 -
[1] 1t9w.a 0
0
0.2 2.2 2.7 1.2 0.6 0 0.1 1.6 0.5 0.6 - 1.5 0.9 2.5 -
[1] 1t9x.a 0.5 1.0
0
2.3 2.0 0.6 0.4 0.1 0 1.5 0.9 0.6 - 1.2 0.5 2.9 -
[1] 2j8s.c 0.5 1.5 0
0.2
1.3 0 0 0 0.1 0 0 0 - 1.3 0.4 1.0 -
[1] 2rdd.a 0.5 1.9 0 6.3
0.3
3.7 0.3 0.1 0 5.9 3.3 3.0 - 0 0 3.2 -
[1] 4dx5.c 0.7 2.0 0 1.0 1.7
0
0 0 0 0 0 0 - 0.9 0.2 0.7 -
[1] 4dx7.c 0.5 1.8 0 0.8 1.6 0
0
0 0 0 0 0 - 1.1 0.2 0.9 -
[1] 4k7q.a 0.5 1.1 0.5 1.9 2.1 3.1 1.1
0
0 2.6 1.8 2.6 - 2.1 1.4 4.0 -
[1] 5jmn.a 0 0 0 1.1 0.8 1.1 0.1 0
0
1.0 0.1 0.1 - 0.5 0.1 0.7 -
[1] 5jmn.c 0.7 2.2 0 1.6 1.2 0 0 0.1 0
0
0.2 0.1 - 0.7 0.1 0.9 -
[1] 5nc5.a 0 0 0 1.7 0.8 1.7 0.2 0 0 1.4
0
0.4 - 0.8 0.2 1.2 -
[1] 5nc5.c 0.9 1.8 0 1.7 1.4 0 0 0.1 0 0 0.1
0
- 1.0 0.3 0.6 -
[2] 2dr6.a 0.5 2.1 0 7.2 2.6 3.8 2.3 0 0.1 3.8 0.8 2.7
-
0.8 0.1 1.5 -
[2] 4u8v.b 0.7 2.3 0 12 0.6 3.9 3.4 0 0 9.3 0.7 2.9 -
0
0.1 1.2 -
[2] 5jmn.b 1.2 3.3 0.8 11 0.9 5.2 1.9 0 0 8.7 0.6 2.6 - 0.1
0
1.9 -
[2] 5nc5.b 0.6 2.4 0 11 1.8 4.9 3.0 0 0 7.9 0.3 2.8 - 1.2 0
0
-
[2] 5yil.b 1.6 3.6 1.6 9.5 1.4 5.5 1.4 0 0 8.5 1.1 2.1 - 0.4 0.5 1.3
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1t9u.a
1t9w.a
1t9x.a
2j8s.c
2rdd.a
4dx5.c
4dx7.c
4k7q.a
5jmn.a
5jmn.c
5nc5.a
5nc5.c
2dr6.a
4u8v.b
5jmn.b
5nc5.b
5yil.b
[1] 1t9u.a
0
.06 .06 .10 .21 .13 .13 .11 .11 .13 .11 .12 .28 .33 .36 .34 .35
[1] 1t9w.a .06
0
.07 .13 .21 .14 .13 .13 .11 .14 .12 .13 .31 .32 .36 .36 .38
[1] 1t9x.a .06 .07
0
.11 .22 .13 .12 .11 .13 .14 .13 .13 .26 .30 .33 .32 .33
[1] 2j8s.c .10 .13 .11
0
.21 .04 .04 .14 .10 .04 .13 .04 .26 .32 .36 .31 .33
[1] 2rdd.a .21 .21 .22 .21
0
.21 .22 .19 .19 .21 .22 .19 .33 .37 .36 .39 .34
[1] 4dx5.c .13 .14 .13 .04 .21
0
.02 .16 .11 .02 .16 .02 .25 .32 .33 .33 .33
[1] 4dx7.c .13 .13 .12 .04 .22 .02
0
.16 .11 .03 .15 .03 .25 .32 .35 .33 .32
[1] 4k7q.a .11 .13 .11 .14 .19 .16 .16
0
.16 .16 .18 .15 .29 .36 .36 .37 .35
[1] 5jmn.a .11 .11 .13 .10 .19 .11 .11 .16
0
.11 .06 .10 .25 .32 .34 .32 .35
[1] 5jmn.c .13 .14 .14 .04 .21 .02 .03 .16 .11
0
.15 .02 .27 .31 .33 .32 .34
[1] 5nc5.a .11 .12 .13 .13 .22 .16 .15 .18 .06 .15
0
.14 .24 .28 .32 .30 .31
[1] 5nc5.c .12 .13 .13 .04 .19 .02 .03 .15 .10 .02 .14
0
.26 .30 .33 .32 .33
[2] 2dr6.a .28 .31 .26 .26 .33 .25 .25 .29 .25 .27 .24 .26
0
.19 .16 .19 .24
[2] 4u8v.b .33 .32 .30 .32 .37 .32 .32 .36 .32 .31 .28 .30 .19
0
.17 .12 .25
[2] 5jmn.b .36 .36 .33 .36 .36 .33 .35 .36 .34 .33 .32 .33 .16 .17
0
.19 .27
[2] 5nc5.b .34 .36 .32 .31 .39 .33 .33 .37 .32 .32 .30 .32 .19 .12 .19
0
.22
[2] 5yil.b .35 .38 .33 .33 .34 .33 .32 .35 .35 .34 .31 .33 .24 .25 .27 .22
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.2 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
1t9u.a
1t9w.a
1t9x.a
2j8s.c
2rdd.a
4dx5.c
4dx7.c
4k7q.a
5jmn.a
5jmn.c
5nc5.a
5nc5.c
2dr6.a
4u8v.b
5jmn.b
5nc5.b
5yil.b
[1] 1t9u.a
0
0.6 0.6 2.3 1.6 2.2 2.3 1.1 3.0 2.2 2.9 2.3 2.9 2.9 3.1 2.9 2.8
[1] 1t9w.a 0.6
0
0.7 2.3 1.6 2.2 2.3 1.1 2.9 2.2 2.9 2.2 3.0 2.9 3.1 2.9 2.8
[1] 1t9x.a 0.6 0.7
0
2.3 1.7 2.2 2.2 1.2 2.9 2.2 2.9 2.2 2.9 2.8 3.0 2.8 2.7
[1] 2j8s.c 2.3 2.3 2.3
0
2.3 0.4 0.4 1.9 2.8 0.5 2.8 0.4 3.2 3.3 3.4 3.2 3.7
[1] 2rdd.a 1.6 1.6 1.7 2.3
0
2.1 2.2 1.5 2.6 2.1 2.6 2.2 2.6 2.6 2.8 2.6 2.7
[1] 4dx5.c 2.2 2.2 2.2 0.4 2.1
0
0.2 1.8 2.7 0.2 2.7 0.3 3.1 3.1 3.2 3.0 3.6
[1] 4dx7.c 2.3 2.3 2.2 0.4 2.2 0.2
0
1.8 2.8 0.3 2.8 0.3 3.2 3.2 3.3 3.1 3.7
[1] 4k7q.a 1.1 1.1 1.2 1.9 1.5 1.8 1.8
0
2.4 1.8 2.4 1.8 2.7 2.8 2.8 2.7 2.4
[1] 5jmn.a 3.0 2.9 2.9 2.8 2.6 2.7 2.8 2.4
0
2.7 0.6 2.7 2.0 2.4 2.0 2.2 2.8
[1] 5jmn.c 2.2 2.2 2.2 0.5 2.1 0.2 0.3 1.8 2.7
0
2.7 0.3 3.1 3.1 3.2 3.0 3.6
[1] 5nc5.a 2.9 2.9 2.9 2.8 2.6 2.7 2.8 2.4 0.6 2.7
0
2.7 2.0 2.3 2.0 2.1 2.8
[1] 5nc5.c 2.3 2.2 2.2 0.4 2.2 0.3 0.3 1.8 2.7 0.3 2.7
0
3.1 3.2 3.3 3.0 3.6
[2] 2dr6.a 2.9 3.0 2.9 3.2 2.6 3.1 3.2 2.7 2.0 3.1 2.0 3.1
0
1.4 1.1 1.3 2.5
[2] 4u8v.b 2.9 2.9 2.8 3.3 2.6 3.1 3.2 2.8 2.4 3.1 2.3 3.2 1.4
0
1.0 0.7 2.1
[2] 5jmn.b 3.1 3.1 3.0 3.4 2.8 3.2 3.3 2.8 2.0 3.2 2.0 3.3 1.1 1.0
0
0.8 2.1
[2] 5nc5.b 2.9 2.9 2.8 3.2 2.6 3.0 3.1 2.7 2.2 3.0 2.1 3.0 1.3 0.7 0.8
0
2.1
[2] 5yil.b 2.8 2.8 2.7 3.7 2.7 3.6 3.7 2.4 2.8 3.6 2.8 3.6 2.5 2.1 2.1 2.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.4 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
1t9u.a
1t9w.a
1t9x.a
2j8s.c
2rdd.a
4dx5.c
4dx7.c
4k7q.a
5jmn.a
5jmn.c
5nc5.a
5nc5.c
2dr6.a
4u8v.b
5jmn.b
5nc5.b
5yil.b
[1] 1t9u.a
0
0.6 0.7 3.3 2.9 3.3 3.3 1.2 3.9 3.3 3.7 3.3 3.7 3.8 4.0 3.8 3.5
[1] 1t9w.a 0.6
0
0.8 3.3 2.8 3.2 3.3 1.2 3.9 3.3 3.7 3.3 3.8 3.8 4.0 3.8 3.4
[1] 1t9x.a 0.7 0.8
0
3.3 2.9 3.3 3.3 1.3 3.9 3.3 3.7 3.3 3.8 3.8 3.9 3.8 3.4
[1] 2j8s.c 3.3 3.3 3.3
0
3.3 0.6 0.6 2.5 3.1 0.9 3.1 0.8 3.5 3.6 3.7 3.6 4.1
[1] 2rdd.a 2.9 2.8 2.9 3.3
0
3.2 3.3 2.2 3.6 3.3 3.6 3.3 3.1 3.3 3.5 3.5 3.2
[1] 4dx5.c 3.3 3.2 3.3 0.6 3.2
0
0.5 2.4 3.1 0.7 3.1 0.7 3.4 3.5 3.6 3.5 4.1
[1] 4dx7.c 3.3 3.3 3.3 0.6 3.3 0.5
0
2.5 3.1 0.8 3.1 0.8 3.5 3.5 3.7 3.5 4.1
[1] 4k7q.a 1.2 1.2 1.3 2.5 2.2 2.4 2.5
0
2.8 2.5 2.8 2.4 3.0 3.1 3.1 3.1 2.8
[1] 5jmn.a 3.9 3.9 3.9 3.1 3.6 3.1 3.1 2.8
0
3.0 0.8 3.0 2.5 2.7 2.5 2.6 3.4
[1] 5jmn.c 3.3 3.3 3.3 0.9 3.3 0.7 0.8 2.5 3.0
0
3.0 0.7 3.5 3.4 3.6 3.4 4.1
[1] 5nc5.a 3.7 3.7 3.7 3.1 3.6 3.1 3.1 2.8 0.8 3.0
0
3.0 2.4 2.5 2.3 2.3 3.0
[1] 5nc5.c 3.3 3.3 3.3 0.8 3.3 0.7 0.8 2.4 3.0 0.7 3.0
0
3.5 3.5 3.6 3.4 4.1
[2] 2dr6.a 3.7 3.8 3.8 3.5 3.1 3.4 3.5 3.0 2.5 3.5 2.4 3.5
0
1.9 1.6 1.9 3.0
[2] 4u8v.b 3.8 3.8 3.8 3.6 3.3 3.5 3.5 3.1 2.7 3.4 2.5 3.5 1.9
0
1.4 1.1 2.7
[2] 5jmn.b 4.0 4.0 3.9 3.7 3.5 3.6 3.7 3.1 2.5 3.6 2.3 3.6 1.6 1.4
0
1.3 2.5
[2] 5nc5.b 3.8 3.8 3.8 3.6 3.5 3.5 3.5 3.1 2.6 3.4 2.3 3.4 1.9 1.1 1.3
0
2.6
[2] 5yil.b 3.5 3.4 3.4 4.1 3.2 4.1 4.1 2.8 3.4 4.1 3.0 4.1 3.0 2.7 2.5 2.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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